From 642686c2e2ff36c8d2e8eeb1679a1765edaef668 Mon Sep 17 00:00:00 2001 From: Peter Huene Date: Mon, 10 Jun 2024 19:57:36 -0700 Subject: [PATCH 1/6] feat: migrate `wdl-gauntlet` to the new parser implementation. This commit removes the use of the existing parser implementation in favor of the new implementation in `wdl-gauntlet`. As a result, `Arena.toml` and `Gauntlet.toml` have been refreshed; in the case of `Arena.toml`, there's a ~10X increase in logged diagnostics due to the new parser implementation successfully parsing files that the existing parser implementation incorrectly parsed with errors. Also added some wall-clock timing for the time spent analyzing a source file and an aggregate duration displayed at the end of gauntlet's output. From the before and after comparisons, the new parser implementation appears to be at least 20X faster in analyzing files, likely due to using `logos` for lexing and the new parser implementation does not backtrack like `pest` does. Also added configuration for ignoring specific files so that `task-templates.wdl` can be excluded as it isn't expected to be valid WDL (it has non-WDL placeholders in it to serve as a template). Once this merges and we're in consensus, removal of the existing parser implementation can begin. --- Arena.toml | 7298 ++++++++++++++++- Cargo.toml | 5 + Gauntlet.toml | 777 +- wdl-gauntlet/CHANGELOG.md | 6 + wdl-gauntlet/Cargo.toml | 16 +- wdl-gauntlet/src/config.rs | 59 +- wdl-gauntlet/src/config/inner.rs | 106 +- wdl-gauntlet/src/config/inner/repr.rs | 29 - wdl-gauntlet/src/config/reportable_concern.rs | 197 - wdl-gauntlet/src/document/identifier.rs | 5 + wdl-gauntlet/src/lib.rs | 394 +- wdl-gauntlet/src/report.rs | 186 +- wdl-gauntlet/src/repository.rs | 27 +- wdl-lint/src/v1.rs | 4 +- 14 files changed, 7655 insertions(+), 1454 deletions(-) delete mode 100644 wdl-gauntlet/src/config/inner/repr.rs delete mode 100644 wdl-gauntlet/src/config/reportable_concern.rs diff --git a/Arena.toml b/Arena.toml index 140395bfe..2952ca80d 100644 --- a/Arena.toml +++ b/Arena.toml @@ -1,358 +1,7184 @@ -version = "v1" +[repositories."ENCODE-DCC/chip-seq-pipeline2"] +identifier = "ENCODE-DCC/chip-seq-pipeline2" +commit_hash = "26eeda81a0540dc793fc69b0c390d232ca7ca50a" + +[repositories."getwilds/ww-fastq-to-cram"] +identifier = "getwilds/ww-fastq-to-cram" +commit_hash = "7dd6c4c7c8c9fc6dcd4eb5ff8f3262cd26d5e7cc" + +[repositories."stjudecloud/workflows"] +identifier = "stjudecloud/workflows" +commit_hash = "a44b18a30fd6192af713fded4bc824f6e77f6ff9" +filters = ["/template/task-templates.wdl"] + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1001:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1002:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1003:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1006:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1007:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1008:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1011:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1012:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1013:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1016:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1017:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1018:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:101:21: warning: input name `fastqs_rep1_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1021:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1022:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1023:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1027:27: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1027:55: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1027:9: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:102:21: warning: input name `fastqs_rep1_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1030:27: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1030:55: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1030:9: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1033:27: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1033:55: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1033:9: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:103:21: warning: input name `fastqs_rep2_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1043:10: warning: private declaration name `ref_fa_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1044:11: warning: private declaration name `bwa_idx_tar_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1046:10: warning: private declaration name `bowtie2_idx_tar_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1047:10: warning: private declaration name `chrsz_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1048:12: warning: private declaration name `gensz_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1049:11: warning: private declaration name `blacklist1_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:104:21: warning: input name `fastqs_rep2_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1051:11: warning: private declaration name `blacklist2_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:105:21: warning: input name `fastqs_rep3_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1064:11: warning: private declaration name `blacklist_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1067:12: warning: private declaration name `mito_chr_name_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1068:12: warning: private declaration name `regex_bfilt_peak_chr_name_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1069:12: warning: private declaration name `genome_name_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:106:21: warning: input name `fastqs_rep3_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1072:12: warning: private declaration name `aligner_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1072:56: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1073:12: warning: private declaration name `peak_caller_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1073:45: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1073:82: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1074:57: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1075:12: warning: private declaration name `peak_type_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1075:42: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1075:53: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1076:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1077:41: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1078:12: warning: private declaration name `idr_rank_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1078:41: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1078:52: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1079:47: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1079:60: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:107:21: warning: input name `fastqs_rep4_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1080:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1082:36: warning: line contains trailing whitespace [rule: Whitespace]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1083:44: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1083:9: warning: private declaration name `cap_num_peak_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1085:9: warning: private declaration name `mapq_thresh_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1086:13: warning: private declaration name `enable_xcor_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1086:46: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1087:13: warning: private declaration name `enable_count_signal_track_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1087:60: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1088:13: warning: private declaration name `enable_jsd_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1088:45: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1089:13: warning: private declaration name `enable_gc_bias_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1089:49: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:108:21: warning: input name `fastqs_rep4_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1090:13: warning: private declaration name `align_only_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1090:45: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1092:11: warning: private declaration name `align_mem_factor_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1092:45: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1094:11: warning: private declaration name `align_disk_factor_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1094:46: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1096:11: warning: private declaration name `call_peak_mem_factor_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1096:53: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1098:11: warning: private declaration name `call_peak_disk_factor_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1098:54: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:109:21: warning: input name `fastqs_rep5_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:10:27: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1102:24: warning: private declaration name `fastqs_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1102:35: warning: line contains trailing whitespace [rule: Whitespace]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:110:21: warning: input name `fastqs_rep5_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:111:21: warning: input name `fastqs_rep6_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:112:21: warning: input name `fastqs_rep6_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1130:24: warning: private declaration name `fastqs_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1130:35: warning: line contains trailing whitespace [rule: Whitespace]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1135:24: warning: private declaration name `ctl_fastqs_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1135:39: warning: line contains trailing whitespace [rule: Whitespace]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:113:21: warning: input name `fastqs_rep7_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:114:21: warning: input name `fastqs_rep7_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:115:21: warning: input name `fastqs_rep8_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1163:24: warning: private declaration name `ctl_fastqs_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1163:39: warning: line contains trailing whitespace [rule: Whitespace]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:116:21: warning: input name `fastqs_rep8_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:117:21: warning: input name `fastqs_rep9_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:118:21: warning: input name `fastqs_rep9_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1193:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1197:42: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1199:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:119:21: warning: input name `fastqs_rep10_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1203:112: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1203:66: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1203:87: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1205:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1209:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:120:21: warning: input name `fastqs_rep10_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1211:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1215:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1217:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1221:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1223:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1230:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1231:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1232:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1233:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1234:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1235:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1239:27: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1241:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1245:27: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1247:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1256:17: warning: private declaration name `paired_end_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1272:39: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1273:38: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1289:15: warning: private declaration name `bam_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1315:15: warning: private declaration name `nodup_bam_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1333:15: warning: private declaration name `ta_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:133:21: warning: input name `ctl_fastqs_rep1_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:134:21: warning: input name `ctl_fastqs_rep1_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:135:21: warning: input name `ctl_fastqs_rep2_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:136:21: warning: input name `ctl_fastqs_rep2_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1379:39: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:137:21: warning: input name `ctl_fastqs_rep3_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1380:38: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:138:21: warning: input name `ctl_fastqs_rep3_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:139:21: warning: input name `ctl_fastqs_rep4_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:13:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:140:21: warning: input name `ctl_fastqs_rep4_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:141:21: warning: input name `ctl_fastqs_rep5_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:142:21: warning: input name `ctl_fastqs_rep5_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:143:21: warning: input name `ctl_fastqs_rep6_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:144:21: warning: input name `ctl_fastqs_rep6_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:145:21: warning: input name `ctl_fastqs_rep7_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:146:21: warning: input name `ctl_fastqs_rep7_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:147:21: warning: input name `ctl_fastqs_rep8_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:148:21: warning: input name `ctl_fastqs_rep8_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1493:14: warning: private declaration name `fraglen_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:149:21: warning: input name `ctl_fastqs_rep9_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1501:17: warning: private declaration name `ctl_paired_end_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:150:21: warning: input name `ctl_fastqs_rep9_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1517:39: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1518:38: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:151:21: warning: input name `ctl_fastqs_rep10_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:152:21: warning: input name `ctl_fastqs_rep10_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1534:15: warning: private declaration name `ctl_bam_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1560:15: warning: private declaration name `ctl_nodup_bam_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1578:15: warning: private declaration name `ctl_ta_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1587:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1598:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:15:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1609:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1620:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:167:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:16:16: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1729:58: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1730:45: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1734:15: warning: private declaration name `peak_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:174:49: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1769:1: warning: line contains only whitespace [rule: Whitespace]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1774:58: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1775:45: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1779:15: warning: private declaration name `peak_pr1_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:177:29: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:17:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1803:58: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1804:45: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1808:15: warning: private declaration name `peak_pr2_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1861:54: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1862:41: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1866:11: warning: private declaration name `peak_pooled_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1867:35: warning: line contains trailing whitespace [rule: Whitespace]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:18:23: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1906:54: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1907:41: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1911:11: warning: private declaration name `peak_ppr1_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1935:54: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1936:41: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1940:11: warning: private declaration name `peak_ppr2_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1948:15: warning: private declaration name `peak1_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1949:15: warning: private declaration name `peak2_` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1953:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1953:46: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1969:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1969:46: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1990:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1990:38: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:1990:58: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2009:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2009:38: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2009:58: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2029:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2046:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2066:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2079:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:20:33: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2167:21: warning: input name `fastqs_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2167:21: warning: task `align` is missing a parameter metadata key for input `fastqs_R1` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2168:21: warning: input name `fastqs_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2168:21: warning: task `align` is missing a parameter metadata key for input `fastqs_R2` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2169:15: warning: task `align` is missing a parameter metadata key for input `ref_fa` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2170:14: warning: task `align` is missing a parameter metadata key for input `trim_bp` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2171:13: warning: task `align` is missing a parameter metadata key for input `crop_length` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2172:13: warning: task `align` is missing a parameter metadata key for input `crop_length_tol` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2173:17: warning: task `align` is missing a parameter metadata key for input `trimmomatic_phred_score_format` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2175:16: warning: task `align` is missing a parameter metadata key for input `aligner` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2177:16: warning: task `align` is missing a parameter metadata key for input `mito_chr_name` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2178:14: warning: task `align` is missing a parameter metadata key for input `multimapping` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2179:15: warning: task `align` is missing a parameter metadata key for input `custom_align_py` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2180:15: warning: task `align` is missing a parameter metadata key for input `idx_tar` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2181:17: warning: task `align` is missing a parameter metadata key for input `paired_end` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2182:17: warning: task `align` is missing a parameter metadata key for input `use_bwa_mem_for_pe` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2183:13: warning: task `align` is missing a parameter metadata key for input `bwa_mem_read_len_limit` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2184:17: warning: task `align` is missing a parameter metadata key for input `use_bowtie2_local_mode` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2186:17: warning: task `align` is missing a parameter metadata key for input `trimmomatic_java_heap` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2187:13: warning: task `align` is missing a parameter metadata key for input `cpu` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2188:15: warning: task `align` is missing a parameter metadata key for input `mem_factor` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2189:13: warning: task `align` is missing a parameter metadata key for input `time_hr` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2190:15: warning: task `align` is missing a parameter metadata key for input `disk_factor` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2192:28: warning: task `align` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2202:5: warning: task `align` uses curly braces in command section [rule: NoCurlyCommands]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2213:34: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2213:54: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2214:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2237:38: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2237:75: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2238:38: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2238:58: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2241:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2243:38: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2243:72: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2244:162: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2244:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2245:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2253:38: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2253:66: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2254:38: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2254:58: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2255:46: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2255:74: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2256:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2257:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2258:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2264:38: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2264:66: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2265:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2266:38: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2266:58: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2267:50: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2267:65: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2268:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2269:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2274:38: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2274:66: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2275:38: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2275:58: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2276:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2277:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2282:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2283:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2284:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2288:25: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2289:25: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2290:32: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2291:34: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2295:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2297:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:22:25: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2308:15: warning: task `filter` is missing a parameter metadata key for input `bam` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2309:17: warning: task `filter` is missing a parameter metadata key for input `paired_end` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2310:15: warning: task `filter` is missing a parameter metadata key for input `ref_fa` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2311:17: warning: task `filter` is missing a parameter metadata key for input `redact_nodup_bam` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2312:16: warning: task `filter` is missing a parameter metadata key for input `dup_marker` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2314:13: warning: task `filter` is missing a parameter metadata key for input `mapq_thresh` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2315:23: warning: task `filter` is missing a parameter metadata key for input `filter_chrs` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2316:14: warning: task `filter` is missing a parameter metadata key for input `chrsz` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2317:17: warning: task `filter` is missing a parameter metadata key for input `no_dup_removal` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2318:16: warning: task `filter` is missing a parameter metadata key for input `mito_chr_name` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2320:13: warning: task `filter` is missing a parameter metadata key for input `cpu` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2321:15: warning: task `filter` is missing a parameter metadata key for input `mem_factor` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2322:17: warning: task `filter` is missing a parameter metadata key for input `picard_java_heap` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2323:13: warning: task `filter` is missing a parameter metadata key for input `time_hr` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2324:15: warning: task `filter` is missing a parameter metadata key for input `disk_factor` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2326:28: warning: task `filter` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2334:5: warning: task `filter` uses curly braces in command section [rule: NoCurlyCommands]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2338:34: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2338:54: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2340:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2341:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2342:33: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2343:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2344:38: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2344:62: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2345:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2346:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2347:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2348:138: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2348:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2353:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2358:31: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2359:31: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2360:32: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2361:28: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2362:39: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2366:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2368:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2378:15: warning: task `bam2ta` is missing a parameter metadata key for input `bam` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2379:17: warning: task `bam2ta` is missing a parameter metadata key for input `paired_end` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2380:16: warning: task `bam2ta` is missing a parameter metadata key for input `mito_chr_name` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2381:13: warning: task `bam2ta` is missing a parameter metadata key for input `subsample` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2383:13: warning: task `bam2ta` is missing a parameter metadata key for input `cpu` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2384:15: warning: task `bam2ta` is missing a parameter metadata key for input `mem_factor` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2385:13: warning: task `bam2ta` is missing a parameter metadata key for input `time_hr` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2386:15: warning: task `bam2ta` is missing a parameter metadata key for input `disk_factor` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2388:28: warning: task `bam2ta` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2395:5: warning: task `bam2ta` uses curly braces in command section [rule: NoCurlyCommands]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:23:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2400:34: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2400:54: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2401:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2402:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2403:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2404:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2407:24: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2411:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2413:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2423:15: warning: task `spr` is missing a parameter metadata key for input `ta` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2424:17: warning: task `spr` is missing a parameter metadata key for input `paired_end` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2425:13: warning: task `spr` is missing a parameter metadata key for input `pseudoreplication_random_seed` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2427:15: warning: task `spr` is missing a parameter metadata key for input `mem_factor` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2428:15: warning: task `spr` is missing a parameter metadata key for input `disk_factor` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2430:28: warning: task `spr` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2436:5: warning: task `spr` uses curly braces in command section [rule: NoCurlyCommands]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2440:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2441:34: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2441:54: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2444:28: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2445:28: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2449:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2451:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2461:22: warning: task `pool_ta` is missing a parameter metadata key for input `tas` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2462:14: warning: task `pool_ta` is missing a parameter metadata key for input `col` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2463:17: warning: task `pool_ta` is missing a parameter metadata key for input `prefix` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2465:28: warning: task `pool_ta` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2468:5: warning: task `pool_ta` uses curly braces in command section [rule: NoCurlyCommands]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2471:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2472:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2473:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2476:31: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2480:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2482:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2492:15: warning: task `xcor` is missing a parameter metadata key for input `ta` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2493:17: warning: task `xcor` is missing a parameter metadata key for input `paired_end` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2494:16: warning: task `xcor` is missing a parameter metadata key for input `mito_chr_name` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2495:13: warning: task `xcor` is missing a parameter metadata key for input `subsample` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2498:17: warning: task `xcor` is missing a parameter metadata key for input `chip_seq_type` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2499:14: warning: task `xcor` is missing a parameter metadata key for input `exclusion_range_min` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:24:23: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2500:14: warning: task `xcor` is missing a parameter metadata key for input `exclusion_range_max` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2502:13: warning: task `xcor` is missing a parameter metadata key for input `cpu` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2503:15: warning: task `xcor` is missing a parameter metadata key for input `mem_factor` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2503:25: warning: line contains trailing whitespace [rule: Whitespace]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2504:13: warning: task `xcor` is missing a parameter metadata key for input `time_hr` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2505:15: warning: task `xcor` is missing a parameter metadata key for input `disk_factor` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2507:28: warning: task `xcor` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2513:5: warning: task `xcor` uses curly braces in command section [rule: NoCurlyCommands]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2517:34: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2517:54: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2518:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2519:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2520:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2521:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2522:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2523:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2524:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2527:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2528:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2529:27: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:252:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2530:33: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2535:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2537:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:253:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2547:22: warning: task `jsd` is missing a parameter metadata key for input `nodup_bams` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2548:22: warning: task `jsd` is missing a parameter metadata key for input `ctl_bams` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2549:15: warning: task `jsd` is missing a parameter metadata key for input `blacklist` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:254:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2550:13: warning: task `jsd` is missing a parameter metadata key for input `mapq_thresh` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2552:13: warning: task `jsd` is missing a parameter metadata key for input `cpu` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2553:15: warning: task `jsd` is missing a parameter metadata key for input `mem_factor` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2554:13: warning: task `jsd` is missing a parameter metadata key for input `time_hr` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2555:15: warning: task `jsd` is missing a parameter metadata key for input `disk_factor` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2557:28: warning: task `jsd` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2563:5: warning: task `jsd` uses curly braces in command section [rule: NoCurlyCommands]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2566:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2567:42: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2567:84: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2568:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2569:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2570:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2573:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2574:36: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2578:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:257:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2580:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:258:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2590:22: warning: task `choose_ctl` is missing a parameter metadata key for input `tas` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2591:22: warning: task `choose_ctl` is missing a parameter metadata key for input `ctl_tas` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2592:15: warning: task `choose_ctl` is missing a parameter metadata key for input `ta_pooled` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2593:15: warning: task `choose_ctl` is missing a parameter metadata key for input `ctl_ta_pooled` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2594:17: warning: task `choose_ctl` is missing a parameter metadata key for input `always_use_pooled_ctl` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2595:15: warning: task `choose_ctl` is missing a parameter metadata key for input `ctl_depth_ratio` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2597:13: warning: task `choose_ctl` is missing a parameter metadata key for input `ctl_depth_limit` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2598:15: warning: task `choose_ctl` is missing a parameter metadata key for input `exp_ctl_depth_ratio_limit` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:259:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2600:28: warning: task `choose_ctl` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2603:5: warning: task `choose_ctl` uses curly braces in command section [rule: NoCurlyCommands]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2606:25: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2607:29: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2608:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2609:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2610:45: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2610:76: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2611:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2612:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2613:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2616:39: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2617:46: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2618:53: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2625:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2627:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:262:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2637:15: warning: task `count_signal_track` is missing a parameter metadata key for input `ta` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2638:14: warning: task `count_signal_track` is missing a parameter metadata key for input `chrsz` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:263:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2640:28: warning: task `count_signal_track` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2644:5: warning: task `count_signal_track` uses curly braces in command section [rule: NoCurlyCommands]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2648:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2649:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:264:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2652:28: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2653:28: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2657:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2659:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2669:15: warning: task `subsample_ctl` is missing a parameter metadata key for input `ta` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2670:17: warning: task `subsample_ctl` is missing a parameter metadata key for input `paired_end` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2671:13: warning: task `subsample_ctl` is missing a parameter metadata key for input `subsample` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2673:15: warning: task `subsample_ctl` is missing a parameter metadata key for input `mem_factor` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2674:15: warning: task `subsample_ctl` is missing a parameter metadata key for input `disk_factor` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2676:28: warning: task `subsample_ctl` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:267:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2682:5: warning: task `subsample_ctl` uses curly braces in command section [rule: NoCurlyCommands]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2685:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2686:34: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2686:54: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2689:35: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:268:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2693:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2695:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:269:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2705:16: warning: task `call_peak` is missing a parameter metadata key for input `peak_caller` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2706:16: warning: task `call_peak` is missing a parameter metadata key for input `peak_type` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2707:22: warning: task `call_peak` is missing a parameter metadata key for input `tas` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2708:13: warning: task `call_peak` is missing a parameter metadata key for input `fraglen` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2709:16: warning: task `call_peak` is missing a parameter metadata key for input `gensz` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2711:14: warning: task `call_peak` is missing a parameter metadata key for input `chrsz` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2712:13: warning: task `call_peak` is missing a parameter metadata key for input `cap_num_peak` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2713:15: warning: task `call_peak` is missing a parameter metadata key for input `pval_thresh` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2714:16: warning: task `call_peak` is missing a parameter metadata key for input `fdr_thresh` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2716:15: warning: task `call_peak` is missing a parameter metadata key for input `blacklist` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2717:17: warning: task `call_peak` is missing a parameter metadata key for input `regex_bfilt_peak_chr_name` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2719:13: warning: task `call_peak` is missing a parameter metadata key for input `cpu` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2719:16: warning: line contains trailing whitespace [rule: Whitespace]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2720:15: warning: task `call_peak` is missing a parameter metadata key for input `mem_factor` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2721:13: warning: task `call_peak` is missing a parameter metadata key for input `time_hr` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2722:15: warning: task `call_peak` is missing a parameter metadata key for input `disk_factor` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2724:28: warning: task `call_peak` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:272:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2730:5: warning: task `call_peak` uses curly braces in command section [rule: NoCurlyCommands]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2735:23: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2736:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2737:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2738:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2739:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:273:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2740:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2741:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2745:23: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2746:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2747:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2748:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2749:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:274:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2750:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2755:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2756:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2756:78: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2757:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2758:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2759:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2760:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2763:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2763:65: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2765:32: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2765:53: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2766:35: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2766:56: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2767:39: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2767:60: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2768:40: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2768:61: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2769:44: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2769:65: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2770:29: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2771:41: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2772:43: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2773:33: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2776:33: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2777:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2779:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:277:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2780:23: warning: line contains trailing whitespace [rule: Whitespace]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:278:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2790:22: warning: task `macs2_signal_track` is missing a parameter metadata key for input `tas` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2791:13: warning: task `macs2_signal_track` is missing a parameter metadata key for input `fraglen` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2792:16: warning: task `macs2_signal_track` is missing a parameter metadata key for input `gensz` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2794:14: warning: task `macs2_signal_track` is missing a parameter metadata key for input `chrsz` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2795:15: warning: task `macs2_signal_track` is missing a parameter metadata key for input `pval_thresh` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2797:15: warning: task `macs2_signal_track` is missing a parameter metadata key for input `mem_factor` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2798:13: warning: task `macs2_signal_track` is missing a parameter metadata key for input `time_hr` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2799:15: warning: task `macs2_signal_track` is missing a parameter metadata key for input `disk_factor` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:279:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2801:28: warning: task `macs2_signal_track` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2807:5: warning: task `macs2_signal_track` uses curly braces in command section [rule: NoCurlyCommands]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2810:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2811:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2812:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2813:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2814:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2815:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2818:29: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2819:27: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2823:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2825:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:282:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2836:16: warning: task `idr` is missing a parameter metadata key for input `prefix` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2837:15: warning: task `idr` is missing a parameter metadata key for input `peak1` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2838:15: warning: task `idr` is missing a parameter metadata key for input `peak2` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2839:15: warning: task `idr` is missing a parameter metadata key for input `peak_pooled` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:283:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2840:15: warning: task `idr` is missing a parameter metadata key for input `idr_thresh` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2841:15: warning: task `idr` is missing a parameter metadata key for input `blacklist` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2842:16: warning: task `idr` is missing a parameter metadata key for input `regex_bfilt_peak_chr_name` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2844:15: warning: task `idr` is missing a parameter metadata key for input `ta` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2845:14: warning: task `idr` is missing a parameter metadata key for input `fraglen` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2846:14: warning: task `idr` is missing a parameter metadata key for input `chrsz` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2847:16: warning: task `idr` is missing a parameter metadata key for input `peak_type` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2848:16: warning: task `idr` is missing a parameter metadata key for input `rank` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:284:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2850:28: warning: task `idr` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2853:5: warning: task `idr` uses curly braces in command section [rule: NoCurlyCommands]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2855:31: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2855:39: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2859:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2860:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2861:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2863:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2864:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2865:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2866:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2866:78: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2867:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2870:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2870:69: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2871:36: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2871:57: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2872:39: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2872:60: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2873:43: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2873:64: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2874:44: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2874:65: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2875:48: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2875:69: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2876:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2877:44: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2878:29: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2879:49: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2879:75: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:287:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2883:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2885:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:288:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2890:6: warning: line contains trailing whitespace [rule: Whitespace]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2895:16: warning: task `overlap` is missing a parameter metadata key for input `prefix` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2896:15: warning: task `overlap` is missing a parameter metadata key for input `peak1` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2897:15: warning: task `overlap` is missing a parameter metadata key for input `peak2` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2898:15: warning: task `overlap` is missing a parameter metadata key for input `peak_pooled` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2899:15: warning: task `overlap` is missing a parameter metadata key for input `blacklist` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:289:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:28:24: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2900:16: warning: task `overlap` is missing a parameter metadata key for input `regex_bfilt_peak_chr_name` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2902:15: warning: task `overlap` is missing a parameter metadata key for input `ta` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2903:14: warning: task `overlap` is missing a parameter metadata key for input `fraglen` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2904:14: warning: task `overlap` is missing a parameter metadata key for input `chrsz` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2905:16: warning: task `overlap` is missing a parameter metadata key for input `peak_type` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2907:28: warning: task `overlap` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:290:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2910:5: warning: task `overlap` uses curly braces in command section [rule: NoCurlyCommands]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2912:31: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2912:39: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2916:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2917:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2918:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2919:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2920:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2922:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2922:78: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2923:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2926:34: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2926:73: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2927:40: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2927:61: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2928:43: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2928:64: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2929:47: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2929:68: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2930:48: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2930:69: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2931:52: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2931:73: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2932:49: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2932:75: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2936:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2938:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:293:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2943:6: warning: line contains trailing whitespace [rule: Whitespace]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2948:16: warning: task `reproducibility` is missing a parameter metadata key for input `prefix` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2949:21: warning: task `reproducibility` is missing a parameter metadata key for input `peaks` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:294:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2953:21: warning: task `reproducibility` is missing a parameter metadata key for input `peaks_pr` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2954:15: warning: task `reproducibility` is missing a parameter metadata key for input `peak_ppr` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2955:16: warning: task `reproducibility` is missing a parameter metadata key for input `peak_type` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2956:14: warning: task `reproducibility` is missing a parameter metadata key for input `chrsz` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2958:28: warning: task `reproducibility` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2961:5: warning: task `reproducibility` uses curly braces in command section [rule: NoCurlyCommands]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2964:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2965:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2966:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2968:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2969:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2972:34: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2973:37: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2974:41: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2975:42: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2976:46: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2977:39: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2978:42: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2979:46: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:297:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2980:47: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2981:51: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2982:40: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2984:41: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2985:43: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2986:33: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:298:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2990:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2992:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:2997:6: warning: line contains trailing whitespace [rule: Whitespace]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:29:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3002:15: warning: task `gc_bias` is missing a parameter metadata key for input `nodup_bam` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3003:14: warning: task `gc_bias` is missing a parameter metadata key for input `ref_fa` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3005:17: warning: task `gc_bias` is missing a parameter metadata key for input `picard_java_heap` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3007:28: warning: task `gc_bias` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3014:5: warning: task `gc_bias` uses curly braces in command section [rule: NoCurlyCommands]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3017:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3018:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3019:138: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3019:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:301:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3022:29: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3023:28: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3027:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3029:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:302:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3040:16: warning: task `qc_report` is missing a parameter metadata key for input `pipeline_ver` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3041:16: warning: task `qc_report` is missing a parameter metadata key for input `title` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3042:16: warning: task `qc_report` is missing a parameter metadata key for input `description` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3043:17: warning: task `qc_report` is missing a parameter metadata key for input `genome` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3046:24: warning: task `qc_report` is missing a parameter metadata key for input `paired_ends` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3047:24: warning: task `qc_report` is missing a parameter metadata key for input `ctl_paired_ends` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3048:16: warning: task `qc_report` is missing a parameter metadata key for input `pipeline_type` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3049:16: warning: task `qc_report` is missing a parameter metadata key for input `aligner` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3050:17: warning: task `qc_report` is missing a parameter metadata key for input `no_dup_removal` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3051:16: warning: task `qc_report` is missing a parameter metadata key for input `peak_caller` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3052:13: warning: task `qc_report` is missing a parameter metadata key for input `cap_num_peak` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3053:15: warning: task `qc_report` is missing a parameter metadata key for input `idr_thresh` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3054:15: warning: task `qc_report` is missing a parameter metadata key for input `pval_thresh` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3055:13: warning: task `qc_report` is missing a parameter metadata key for input `xcor_trim_bp` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3056:13: warning: task `qc_report` is missing a parameter metadata key for input `xcor_subsample_reads` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3058:21: warning: task `qc_report` is missing a parameter metadata key for input `samstat_qcs` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3059:21: warning: task `qc_report` is missing a parameter metadata key for input `nodup_samstat_qcs` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:305:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3060:21: warning: task `qc_report` is missing a parameter metadata key for input `dup_qcs` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3061:21: warning: task `qc_report` is missing a parameter metadata key for input `lib_complexity_qcs` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3062:21: warning: task `qc_report` is missing a parameter metadata key for input `ctl_samstat_qcs` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3063:21: warning: task `qc_report` is missing a parameter metadata key for input `ctl_nodup_samstat_qcs` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3064:21: warning: task `qc_report` is missing a parameter metadata key for input `ctl_dup_qcs` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3065:21: warning: task `qc_report` is missing a parameter metadata key for input `ctl_lib_complexity_qcs` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3066:21: warning: task `qc_report` is missing a parameter metadata key for input `xcor_plots` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3067:21: warning: task `qc_report` is missing a parameter metadata key for input `xcor_scores` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3068:15: warning: task `qc_report` is missing a parameter metadata key for input `jsd_plot` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3069:21: warning: task `qc_report` is missing a parameter metadata key for input `jsd_qcs` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:306:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3070:21: warning: task `qc_report` is missing a parameter metadata key for input `idr_plots` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3071:21: warning: task `qc_report` is missing a parameter metadata key for input `idr_plots_pr` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3072:15: warning: task `qc_report` is missing a parameter metadata key for input `idr_plot_ppr` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3073:21: warning: task `qc_report` is missing a parameter metadata key for input `frip_qcs` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3074:21: warning: task `qc_report` is missing a parameter metadata key for input `frip_qcs_pr1` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3075:21: warning: task `qc_report` is missing a parameter metadata key for input `frip_qcs_pr2` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3076:15: warning: task `qc_report` is missing a parameter metadata key for input `frip_qc_pooled` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3077:15: warning: task `qc_report` is missing a parameter metadata key for input `frip_qc_ppr1` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3077:27: warning: line contains trailing whitespace [rule: Whitespace]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3078:15: warning: task `qc_report` is missing a parameter metadata key for input `frip_qc_ppr2` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3078:27: warning: line contains trailing whitespace [rule: Whitespace]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3079:21: warning: task `qc_report` is missing a parameter metadata key for input `frip_idr_qcs` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3080:21: warning: task `qc_report` is missing a parameter metadata key for input `frip_idr_qcs_pr` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3081:15: warning: task `qc_report` is missing a parameter metadata key for input `frip_idr_qc_ppr` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3081:30: warning: line contains trailing whitespace [rule: Whitespace]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3082:21: warning: task `qc_report` is missing a parameter metadata key for input `frip_overlap_qcs` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3083:21: warning: task `qc_report` is missing a parameter metadata key for input `frip_overlap_qcs_pr` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3084:15: warning: task `qc_report` is missing a parameter metadata key for input `frip_overlap_qc_ppr` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3085:15: warning: task `qc_report` is missing a parameter metadata key for input `idr_reproducibility_qc` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3086:15: warning: task `qc_report` is missing a parameter metadata key for input `overlap_reproducibility_qc` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3088:21: warning: task `qc_report` is missing a parameter metadata key for input `gc_plots` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3090:21: warning: task `qc_report` is missing a parameter metadata key for input `peak_region_size_qcs` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3091:21: warning: task `qc_report` is missing a parameter metadata key for input `peak_region_size_plots` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3092:21: warning: task `qc_report` is missing a parameter metadata key for input `num_peak_qcs` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3094:15: warning: task `qc_report` is missing a parameter metadata key for input `idr_opt_peak_region_size_qc` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3095:15: warning: task `qc_report` is missing a parameter metadata key for input `idr_opt_peak_region_size_plot` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3096:15: warning: task `qc_report` is missing a parameter metadata key for input `idr_opt_num_peak_qc` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3098:15: warning: task `qc_report` is missing a parameter metadata key for input `overlap_opt_peak_region_size_qc` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3099:15: warning: task `qc_report` is missing a parameter metadata key for input `overlap_opt_peak_region_size_plot` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:309:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3100:15: warning: task `qc_report` is missing a parameter metadata key for input `overlap_opt_num_peak_qc` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3102:15: warning: task `qc_report` is missing a parameter metadata key for input `qc_json_ref` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3104:28: warning: task `qc_report` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3107:5: warning: task `qc_report` uses curly braces in command section [rule: NoCurlyCommands]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:310:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3111:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3114:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3115:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3116:33: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3117:37: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3120:40: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3120:65: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3122:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3127:33: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3128:39: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3129:29: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3130:40: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3131:32: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3132:33: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3133:31: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3134:34: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3135:37: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3136:43: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3137:33: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3138:44: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3139:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:313:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3140:29: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3141:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3142:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3143:34: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3144:34: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3145:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3146:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3147:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3148:34: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3149:37: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:314:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3150:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3151:38: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3152:41: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3153:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3154:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3155:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3156:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3157:42: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3158:44: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3159:34: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:315:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3160:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3161:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3162:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3163:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3164:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3165:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3168:15: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3171:28: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3172:29: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3173:49: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3173:75: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3177:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3179:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3184:6: warning: line contains trailing whitespace [rule: Whitespace]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:318:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3190:15: warning: task `read_genome_tsv` is missing a parameter metadata key for input `genome_tsv` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3191:17: warning: task `read_genome_tsv` is missing a parameter metadata key for input `null_s` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3193:28: warning: task `read_genome_tsv` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:319:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:320:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3214:43: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3215:34: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3215:76: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3216:39: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3216:86: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3217:43: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3217:94: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3218:33: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3218:74: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3219:33: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3219:74: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3220:37: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3220:82: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3221:38: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3221:84: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3222:41: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3222:90: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3223:53: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3223:90: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3224:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3229:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3231:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3231:36: warning: line contains trailing whitespace [rule: Whitespace]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:323:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3241:20: warning: task `rounded_mean` is missing a parameter metadata key for input `ints` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3243:28: warning: task `rounded_mean` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3247:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:324:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3258:37: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:325:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3262:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3264:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3274:16: warning: task `raise_exception` is missing a parameter metadata key for input `msg` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3276:28: warning: task `raise_exception` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3278:5: warning: task `raise_exception` uses curly braces in command section [rule: NoCurlyCommands]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3283:28: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3288:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:328:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:3290:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:329:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:32:24: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:330:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:333:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:334:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:337:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:338:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:339:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:33:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:343:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:344:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:345:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:348:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:349:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:350:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:352:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:356:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:357:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:358:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:360:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:364:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:365:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:366:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:368:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:36:24: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:372:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:373:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:374:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:376:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:37:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:380:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:381:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:382:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:385:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:386:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:387:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:38:23: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:390:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:391:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:392:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:395:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:396:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:397:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:400:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:401:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:402:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:405:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:406:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:407:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:410:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:411:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:412:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:415:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:416:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:417:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:41:24: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:420:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:421:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:422:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:425:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:426:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:427:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:42:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:430:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:431:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:432:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:435:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:436:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:437:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:43:23: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:440:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:441:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:442:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:445:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:446:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:447:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:450:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:451:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:452:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:455:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:456:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:457:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:460:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:461:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:462:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:465:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:466:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:467:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:46:24: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:470:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:471:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:472:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:475:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:476:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:477:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:47:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:480:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:481:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:482:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:485:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:486:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:487:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:48:23: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:490:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:491:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:492:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:495:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:496:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:497:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:500:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:501:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:502:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:506:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:507:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:508:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:511:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:512:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:513:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:516:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:517:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:518:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:51:24: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:520:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:524:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:525:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:526:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:528:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:52:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:532:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:533:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:534:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:536:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:53:23: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:540:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:541:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:542:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:544:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:548:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:549:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:550:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:553:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:554:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:555:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:558:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:559:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:560:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:563:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:564:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:565:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:568:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:569:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:56:24: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:570:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:573:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:574:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:575:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:578:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:579:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:57:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:580:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:583:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:584:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:585:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:588:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:589:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:58:23: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:590:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:593:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:594:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:595:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:598:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:599:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:600:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:603:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:604:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:605:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:608:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:609:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:610:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:613:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:614:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:615:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:618:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:619:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:61:24: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:620:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:623:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:624:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:625:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:628:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:629:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:62:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:630:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:633:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:634:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:635:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:638:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:639:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:63:23: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:640:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:644:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:645:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:646:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:647:23: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:647:29: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:647:40: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:648:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:651:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:652:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:653:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:656:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:657:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:658:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:661:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:662:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:663:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:666:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:667:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:66:24: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:670:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:671:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:674:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:675:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:679:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:67:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:680:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:681:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:682:23: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:682:34: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:682:41: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:683:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:686:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:687:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:688:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:68:23: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:691:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:692:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:693:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:696:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:697:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:698:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:701:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:702:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:703:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:706:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:707:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:708:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:711:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:712:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:713:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:716:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:717:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:718:23: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:718:31: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:718:42: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:719:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:722:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:723:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:724:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:727:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:728:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:729:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:732:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:733:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:734:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:735:23: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:735:33: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:736:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:739:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:740:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:741:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:744:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:745:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:746:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:749:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:74:25: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:750:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:751:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:754:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:755:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:756:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:759:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:75:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:760:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:761:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:764:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:765:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:766:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:769:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:76:24: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:770:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:771:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:774:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:775:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:776:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:779:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:77:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:780:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:781:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:784:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:785:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:786:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:789:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:78:28: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:790:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:791:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:794:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:795:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:796:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:799:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:800:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:801:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:802:22: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:805:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:806:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:807:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:810:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:811:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:812:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:816:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:817:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:818:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:81:24: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:821:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:822:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:823:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:826:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:827:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:828:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:82:30: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:831:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:832:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:836:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:837:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:838:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:841:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:842:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:843:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:846:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:847:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:848:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:851:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:852:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:853:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:856:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:857:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:858:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:861:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:862:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:863:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:866:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:867:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:868:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:871:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:872:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:873:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:876:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:877:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:878:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:881:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:882:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:883:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:886:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:887:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:888:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:88:15: warning: workflow `chip` is missing a parameter metadata key for input `bwa_idx_tar` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:891:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:892:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:893:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:896:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:897:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:898:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:901:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:902:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:903:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:906:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:907:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:908:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:911:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:912:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:913:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:916:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:917:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:918:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:921:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:922:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:923:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:926:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:927:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:928:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:931:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:932:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:933:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:936:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:937:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:938:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:941:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:942:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:943:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:946:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:947:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:948:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:951:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:952:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:953:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:956:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:957:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:958:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:961:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:962:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:963:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:966:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:967:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:968:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:971:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:972:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:973:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:976:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:977:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:978:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:981:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:982:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:983:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:986:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:987:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:988:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:991:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:992:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:993:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:996:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:997:20: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" +message = "/chip.wdl:998:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/compare_md5sum.wdl" +message = "/dev/test/test_task/compare_md5sum.wdl:4:20: warning: task `compare_md5sum` is missing a parameter metadata key for input `labels` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/compare_md5sum.wdl" +message = "/dev/test/test_task/compare_md5sum.wdl:5:18: warning: task `compare_md5sum` is missing a parameter metadata key for input `files` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/compare_md5sum.wdl" +message = "/dev/test/test_task/compare_md5sum.wdl:6:18: warning: task `compare_md5sum` is missing a parameter metadata key for input `ref_files` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/compare_md5sum.wdl" +message = "/dev/test/test_task/compare_md5sum.wdl:84:45: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/compare_md5sum.wdl" +message = "/dev/test/test_task/compare_md5sum.wdl:85:46: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/compare_md5sum.wdl" +message = "/dev/test/test_task/compare_md5sum.wdl:86:26: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/compare_md5sum.wdl" +message = "/dev/test/test_task/compare_md5sum.wdl:87:39: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/compare_md5sum.wdl" +message = "/dev/test/test_task/compare_md5sum.wdl:91:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/compare_md5sum.wdl" +message = "/dev/test/test_task/compare_md5sum.wdl:93:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" +message = "/dev/test/test_task/test_bam2ta.wdl:10:16: warning: workflow `test_bam2ta` is missing a parameter metadata key for input `se_nodup_bam` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" +message = "/dev/test/test_task/test_bam2ta.wdl:12:16: warning: workflow `test_bam2ta` is missing a parameter metadata key for input `ref_pe_ta` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" +message = "/dev/test/test_task/test_bam2ta.wdl:13:16: warning: workflow `test_bam2ta` is missing a parameter metadata key for input `ref_pe_ta_subsample` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" +message = "/dev/test/test_task/test_bam2ta.wdl:14:16: warning: workflow `test_bam2ta` is missing a parameter metadata key for input `ref_se_ta` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" +message = "/dev/test/test_task/test_bam2ta.wdl:15:16: warning: workflow `test_bam2ta` is missing a parameter metadata key for input `ref_se_ta_subsample` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" +message = "/dev/test/test_task/test_bam2ta.wdl:16:16: warning: workflow `test_bam2ta` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" +message = "/dev/test/test_task/test_bam2ta.wdl:23:28: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" +message = "/dev/test/test_task/test_bam2ta.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" +message = "/dev/test/test_task/test_bam2ta.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" +message = "/dev/test/test_task/test_bam2ta.wdl:7:13: warning: workflow `test_bam2ta` is missing a parameter metadata key for 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warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:152:10: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:153:10: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:154:10: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:156:10: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] 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"ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:160:10: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:162:10: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:163:10: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:164:10: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:166:10: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:167:10: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:168:10: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:169:10: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:16:13: warning: workflow `test_choose_ctl` is 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"ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:184:10: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:185:10: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:186:10: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:187:10: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:188:10: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:18:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_sub2` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:19:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_sub_pooled` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:203:1: warning: more than one blank line in a row [rule: Whitespace]" + +[[diagnostics]] +document = 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"/dev/test/test_task/test_choose_ctl.wdl:211:5: warning: task `raise_exception_and_print` uses curly braces in command section [rule: NoCurlyCommands]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:213:32: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:217:28: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:21:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_always_use_pooled_ctl_idx1` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:222:18: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:224:17: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:22:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_always_use_pooled_ctl_idx2` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:23:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_always_use_pooled_ctl_sub1` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:24:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_always_use_pooled_ctl_sub2` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:25:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_always_use_pooled_ctl_sub_pooled` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:27:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_single_rep_idx1` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:28:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_single_rep_sub1` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:29:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_single_rep_sub_pooled` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = 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"ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:34:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_single_ctl_sub2` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:35:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_single_ctl_sub_pooled` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:37:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_disabled_idx1` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:38:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_disabled_idx2` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:39:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_disabled_sub1` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:40:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_disabled_sub2` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:41:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_disabled_sub_pooled` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:43:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_ctl_depth_limit_only_idx1` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:44:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_ctl_depth_limit_only_idx2` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:45:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_ctl_depth_limit_only_sub1` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:46:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_ctl_depth_limit_only_sub2` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" +message = "/dev/test/test_task/test_choose_ctl.wdl:47:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input 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"/dev/test/test_task/test_trimmomatic.wdl:120:13: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:121:13: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:122:13: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:12:13: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `se_crop_length` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:13:13: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `pe_crop_length_tol` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:14:13: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `se_crop_length_tol` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:17:14: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `ref_pe_cropped_flagstat` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:18:14: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `ref_se_cropped_flagstat` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:19:14: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `ref_pe_cropped_phred33_flagstat` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:20:14: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `ref_se_cropped_phred64_flagstat` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:22:14: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `pe_bowtie2_idx_tar` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:23:14: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `se_bowtie2_idx_tar` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:24:16: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:38:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:40:25: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:57:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:59:25: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:77:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:79:25: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:7:21: warning: input name `pe_fastqs_R1` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:7:21: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `pe_fastqs_R1` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:88:42: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:8:21: warning: input name `pe_fastqs_R2` is not snake_case [rule: SnakeCase]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:8:21: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `pe_fastqs_R2` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:97:19: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:99:25: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" +message = "/dev/test/test_task/test_trimmomatic.wdl:9:21: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `se_fastqs` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" +message = "/dev/test/test_task/test_xcor.wdl:10:16: warning: workflow `test_xcor` is missing a parameter metadata key for input `pe_ta` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" +message = "/dev/test/test_task/test_xcor.wdl:11:16: warning: workflow `test_xcor` is missing a parameter metadata key for input `se_ta` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" +message = "/dev/test/test_task/test_xcor.wdl:13:16: warning: workflow `test_xcor` is missing a parameter metadata key for input `ref_pe_xcor_log` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" +message = "/dev/test/test_task/test_xcor.wdl:14:16: warning: workflow `test_xcor` is missing a parameter metadata key for input `ref_pe_xcor_log_subsample` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" +message = "/dev/test/test_task/test_xcor.wdl:15:16: warning: workflow `test_xcor` is missing a parameter metadata key for input `ref_se_xcor_log` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" +message = "/dev/test/test_task/test_xcor.wdl:16:16: warning: workflow `test_xcor` is missing a parameter metadata key for input `ref_se_xcor_log_subsample` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" +message = "/dev/test/test_task/test_xcor.wdl:17:16: warning: workflow `test_xcor` is missing a parameter metadata key for input `mito_chr_name` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" +message = "/dev/test/test_task/test_xcor.wdl:17:32: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" +message = "/dev/test/test_task/test_xcor.wdl:18:16: warning: workflow `test_xcor` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" +message = "/dev/test/test_task/test_xcor.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" +message = "/dev/test/test_task/test_xcor.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" +message = "/dev/test/test_task/test_xcor.wdl:7:13: warning: workflow `test_xcor` is missing a parameter metadata key for input `xcor_subsample` [rule: MatchingParameterMeta]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" +message = "/dev/test/test_task/test_xcor.wdl:81:13: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" +message = "/dev/test/test_task/test_xcor.wdl:82:13: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" +message = "/dev/test/test_task/test_xcor.wdl:83:13: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" +message = "/dev/test/test_task/test_xcor.wdl:84:13: warning: string defined with single quotes [rule: DoubleQuotes]" + +[[diagnostics]] +document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" +message = "/dev/test/test_task/test_xcor.wdl:8:13: warning: workflow `test_xcor` is missing a parameter metadata key for input `xcor_subsample_default` [rule: MatchingParameterMeta]" + +[[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "[v1::W001::[Spacing, Style]::Low] trailing space (8:42)" +message = "/ww-fastq-to-cram.wdl:129:5: note: task `FastqToUnmappedBam` has an extraneous parameter metadata key named `unmapped_bam` [rule: MatchingParameterMeta]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "[v1::W003::[Completeness]::Medium] extraneous parameter meta within task: crai (203:5-203:9)" +message = "/ww-fastq-to-cram.wdl:134:6: warning: task name `ValidateCram` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "[v1::W003::[Completeness]::Medium] extraneous parameter meta within task: cram (202:5-202:9)" +message = "/ww-fastq-to-cram.wdl:165:5: note: task `ValidateCram` has an extraneous parameter metadata key named `validation` [rule: MatchingParameterMeta]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "[v1::W003::[Completeness]::Medium] extraneous parameter meta within task: unmapped_bam (129:5-129:17)" +message = "/ww-fastq-to-cram.wdl:170:6: warning: task name `MergeBamsToCram` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "[v1::W003::[Completeness]::Medium] extraneous parameter meta within task: validation (165:5-165:15)" +message = "/ww-fastq-to-cram.wdl:202:5: note: task `MergeBamsToCram` has an extraneous parameter metadata key named `cram` [rule: MatchingParameterMeta]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "[v1::W003::[Completeness]::Medium] extraneous parameter meta within workflow: unmapped_cram_indexes (75:5-75:26)" +message = "/ww-fastq-to-cram.wdl:203:5: note: task `MergeBamsToCram` has an extraneous parameter metadata key named `crai` [rule: MatchingParameterMeta]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "[v1::W003::[Completeness]::Medium] extraneous parameter meta within workflow: unmapped_crams (74:5-74:19)" +message = "/ww-fastq-to-cram.wdl:205:1: warning: missing newline at the end of the file [rule: EndingNewline]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "[v1::W003::[Completeness]::Medium] extraneous parameter meta within workflow: validation (76:5-76:15)" +message = "/ww-fastq-to-cram.wdl:23:10: warning: workflow name `PairedFastqsToUnmappedCram` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (134:6-134:18)" +message = "/ww-fastq-to-cram.wdl:57:13: warning: line contains trailing whitespace [rule: Whitespace]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (170:6-170:21)" +message = "/ww-fastq-to-cram.wdl:74:5: note: workflow `PairedFastqsToUnmappedCram` has an extraneous parameter metadata key named `unmapped_crams` [rule: MatchingParameterMeta]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (23:10-23:36)" +message = "/ww-fastq-to-cram.wdl:75:5: note: workflow `PairedFastqsToUnmappedCram` has an extraneous parameter metadata key named `unmapped_cram_indexes` [rule: MatchingParameterMeta]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (83:6-83:24)" +message = "/ww-fastq-to-cram.wdl:76:5: note: workflow `PairedFastqsToUnmappedCram` has an extraneous parameter metadata key named `validation` [rule: MatchingParameterMeta]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "[v1::W007::[Spacing, Style]::Low] missing newline at the end of the file (205:2-205:2)" +message = "/ww-fastq-to-cram.wdl:83:6: warning: task name `FastqToUnmappedBam` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (32:12-32:14)" +message = "/data_structures/read_group.wdl:32:12: warning: struct member name `ID` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (33:13-33:15)" +message = "/data_structures/read_group.wdl:33:13: warning: struct member name `BC` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (34:13-34:15)" +message = "/data_structures/read_group.wdl:34:13: warning: struct member name `CN` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (35:13-35:15)" +message = "/data_structures/read_group.wdl:35:13: warning: struct member name `DS` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (36:13-36:15)" +message = "/data_structures/read_group.wdl:36:13: warning: struct member name `DT` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (37:13-37:15)" +message = "/data_structures/read_group.wdl:37:13: warning: struct member name `FO` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (38:13-38:15)" +message = "/data_structures/read_group.wdl:38:13: warning: struct member name `KS` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (39:13-39:15)" +message = "/data_structures/read_group.wdl:39:13: warning: struct member name `LB` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (40:13-40:15)" +message = "/data_structures/read_group.wdl:40:13: warning: struct member name `PG` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (41:10-41:12)" +message = "/data_structures/read_group.wdl:41:10: warning: struct member name `PI` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (42:13-42:15)" +message = "/data_structures/read_group.wdl:42:13: warning: struct member name `PL` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (43:13-43:15)" +message = "/data_structures/read_group.wdl:43:13: warning: struct member name `PM` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (44:13-44:15)" +message = "/data_structures/read_group.wdl:44:13: warning: struct member name `PU` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (45:13-45:15)" +message = "/data_structures/read_group.wdl:45:13: warning: struct member name `SM` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (107:14-107:23)" +message = "/tools/gatk4.wdl:107:14: warning: input name `dbSNP_vcf` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (108:14-108:29)" +message = "/tools/gatk4.wdl:108:14: warning: input name `dbSNP_vcf_index` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (249:14-249:23)" +message = "/tools/gatk4.wdl:249:14: warning: input name `dbSNP_vcf` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (250:14-250:29)" +message = "/tools/gatk4.wdl:250:14: warning: input name `dbSNP_vcf_index` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (552:13-552:34)" +message = "/tools/star.wdl:552:13: warning: input name `out_QS_conversion_add` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (553:13-553:34)" +message = "/tools/star.wdl:553:13: warning: input name `out_sam_attr_IH_start` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (555:13-555:28)" +message = "/tools/star.wdl:555:13: warning: input name `out_sam_flag_OR` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (556:13-556:29)" +message = "/tools/star.wdl:556:13: warning: input name `out_sam_flag_AND` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (564:13-564:27)" +message = "/tools/star.wdl:564:13: warning: input name `score_gap_GCAG` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (565:13-565:27)" +message = "/tools/star.wdl:565:13: warning: input name `score_gap_ATAC` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (597:13-597:40)" +message = "/tools/star.wdl:597:13: warning: input name `chim_score_junction_nonGTAG` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (61:13-61:36)" +message = "/tools/star.wdl:61:13: warning: input name `genome_SA_index_n_bases` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (62:13-62:31)" +message = "/tools/star.wdl:62:13: warning: input name `genome_SA_sparse_d` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (818:9-818:30)" +message = "/tools/star.wdl:818:9: warning: struct member name `GT_AG_and_CT_AC_motif` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (819:9-819:30)" +message = "/tools/star.wdl:819:9: warning: struct member name `GC_AG_and_CT_GC_motif` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (820:9-820:30)" +message = "/tools/star.wdl:820:9: warning: struct member name `AT_AC_and_GT_AT_motif` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" -document = "stjudecloud/workflows:/tools/util.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (413:14-413:21)" - -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (101:15-101:24)" +message = "/workflows/reference/gatk-reference.wdl:101:15: warning: output name `dbSNP_vcf` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (102:15-102:30)" +message = "/workflows/reference/gatk-reference.wdl:102:15: warning: output name `dbSNP_vcf_index` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (40:16-40:29)" +message = "/workflows/reference/gatk-reference.wdl:40:16: warning: input name `dbSNP_vcf_url` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (41:16-41:30)" +message = "/workflows/reference/gatk-reference.wdl:41:16: warning: input name `dbSNP_vcf_name` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (42:17-42:36)" +message = "/workflows/reference/gatk-reference.wdl:42:17: warning: input name `dbSNP_vcf_index_url` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (43:17-43:37)" - -[[concerns]] -kind = "LintWarning" -document = "stjudecloud/workflows:/workflows/reference/make-qc-reference.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (125:14-125:21)" +message = "/workflows/reference/gatk-reference.wdl:43:17: warning: input name `dbSNP_vcf_index_name` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (138:13-138:40)" +message = "/workflows/rnaseq/rnaseq-core.wdl:138:13: warning: input name `chim_score_junction_nonGTAG` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (42:14-42:23)" +message = "/workflows/rnaseq/rnaseq-variant-calling.wdl:42:14: warning: input name `dbSNP_vcf` is not snake_case [rule: SnakeCase]" -[[concerns]] -kind = "LintWarning" +[[diagnostics]] document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl" -message = "[v1::W006::[Naming, Style, Clarity]::Medium] identifier must be snake case (43:14-43:29)" +message = "/workflows/rnaseq/rnaseq-variant-calling.wdl:43:14: warning: input name `dbSNP_vcf_index` is not snake_case [rule: SnakeCase]" diff --git a/Cargo.toml b/Cargo.toml index f10d6393a..852b1d51e 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -41,3 +41,8 @@ pretty_assertions = "1.4.0" rayon = "1.10.0" approx = "0.5.1" codespan-reporting = "0.11.1" +anyhow = "1.0.86" +dirs = "5.0.1" +faster-hex = "0.9.0" +git2 = "0.18.3" +temp-dir = "0.1.13" diff --git a/Gauntlet.toml b/Gauntlet.toml index 69684ee23..aebe5ef83 100644 --- a/Gauntlet.toml +++ b/Gauntlet.toml @@ -1,5 +1,3 @@ -version = "v1" - [repositories."ENCODE-DCC/chip-seq-pipeline2"] identifier = "ENCODE-DCC/chip-seq-pipeline2" commit_hash = "26eeda81a0540dc793fc69b0c390d232ca7ca50a" @@ -22,15 +20,15 @@ commit_hash = "04057c175d0307f96f3f90e2704a4594ebf4e314" [repositories."broadinstitute/palantir-workflows"] identifier = "broadinstitute/palantir-workflows" -commit_hash = "4d28b6d381b765a12e9f838d305e39eddba1c9c7" +commit_hash = "f211198dd142d5aaadaa69fa6dc4f97a4bb2f8b3" [repositories."broadinstitute/warp"] identifier = "broadinstitute/warp" -commit_hash = "a22865d02b2f674da388c472654a73599afb94ed" +commit_hash = "f094475689311ccf227b39b5f40b70762889566c" [repositories."chanzuckerberg/czid-workflows"] identifier = "chanzuckerberg/czid-workflows" -commit_hash = "6ed1fc2ec1aa477b38ca45f0a39fa6402d2a0163" +commit_hash = "0381416a3e855d7a036322464f09c8f087d1c5ba" [repositories."getwilds/ww-fastq-to-cram"] identifier = "getwilds/ww-fastq-to-cram" @@ -46,658 +44,309 @@ commit_hash = "ee08634f28810e5d6fd1a904fc83f4e67821550e" [repositories."stjudecloud/workflows"] identifier = "stjudecloud/workflows" -commit_hash = "2970ed4ffec95cbc3c94b3e85543d46c4e730f71" +commit_hash = "a44b18a30fd6192af713fded4bc824f6e77f6ff9" +filters = ["/template/task-templates.wdl"] [repositories."theiagen/public_health_bioinformatics"] identifier = "theiagen/public_health_bioinformatics" -commit_hash = "dce427204424361a17c084224727e9df1e00eb63" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "The following tokens are required: comma. (1262:26)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" -message = "The following tokens are required: comma. (30:37)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "The following tokens are required: comma. (32:37)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "The following tokens are required: comma. (33:37)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl" -message = "The following tokens are required: comma. (31:33)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "The following tokens are required: comma. (66:45)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_count_signal_track.wdl" -message = "The following tokens are required: comma. (21:61)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "The following tokens are required: comma. (33:37)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_gc_bias.wdl" -message = "The following tokens are required: comma. (18:25)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "The following tokens are required: comma. (31:31)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_jsd.wdl" -message = "The following tokens are required: comma. (27:31)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "The following tokens are required: comma. (36:39)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2_signal_track.wdl" -message = "The following tokens are required: comma. (29:61)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_overlap.wdl" -message = "The following tokens are required: comma. (30:39)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_pool_ta.wdl" -message = "The following tokens are required: comma. (19:39)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_reproducibility.wdl" -message = "The following tokens are required: comma. (22:55)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spp.wdl" -message = "The following tokens are required: comma. (35:37)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spr.wdl" -message = "The following tokens are required: comma. (28:31)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_subsample_ctl.wdl" -message = "The following tokens are required: comma. (25:51)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "The following tokens are required: comma. (37:45)" - -[[concerns]] -kind = "ParseError" -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" -message = "The following tokens are required: comma. (30:33)" - -[[concerns]] -kind = "ParseError" +commit_hash = "092f19a0f610eb0a01757456932519bbbfe2bbd9" + +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl" +message = "/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl:112:40: error: expected input section, output section, runtime section, metadata section, parameter metadata section, conditional statement, scatter statement, task call statement, or private declaration, but found `{`" + +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl" +message = "/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl:112:67: error: expected declaration name, but found `,`" + +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl" +message = "/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl:113:62: error: expected declaration name, but found `,`" + +[[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl" -message = "The following tokens are required: singular_identifier. (112:41)" +message = "/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl:114:71: error: expected declaration name, but found `*`" -[[concerns]] -kind = "ParseError" +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl" +message = "/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl:115:72: error: expected declaration name, but found `*`" + +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl" +message = "/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl:117:5: error: expected import statement, struct definition, task definition, or workflow definition, but found `call` keyword" + +[[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" -message = "The following tokens are required: singular_identifier, or, and, add, sub, mul, div, remainder, eq, neq, lte, gte, lt, gt, member, index, call. (110:29)" +message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:110:29: error: expected runtime key, but found `,`" -[[concerns]] -kind = "ParseError" -document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl" -message = "The following tokens are required: singular_identifier, or, and, add, sub, mul, div, remainder, eq, neq, lte, gte, lt, gt, member, index, call. (58:29)" +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" +message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:111:23: error: expected runtime key, but found `,`" -[[concerns]] -kind = "ParseError" -document = "broadinstitute/palantir-workflows:/BenchmarkVCFs/BenchmarkVCFs.wdl" -message = "The following tokens are required: singular_identifier. (271:111)" +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" +message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:142:29: error: expected runtime key, but found `,`" -[[concerns]] -kind = "ParseError" -document = "broadinstitute/palantir-workflows:/HaplotypeMap/BuildHaplotypeMap.wdl" -message = "The following tokens are required: version. (17:1)" - -[[concerns]] -kind = "ParseError" -document = "broadinstitute/palantir-workflows:/ImputationPipeline/AggregatePRSResults.wdl" -message = "The following tokens are required: or, and, add, sub, mul, div, remainder, eq, neq, lte, gte, lt, gt, member, index, call. (217:82)" - -[[concerns]] -kind = "ParseError" -document = "broadinstitute/palantir-workflows:/ImputationPipeline/EndToEndPipeline.wdl" -message = "The following tokens are required: comma. (76:4)" - -[[concerns]] -kind = "ParseError" -document = "broadinstitute/palantir-workflows:/ImputationPipeline/Validation/ValidateImputation.wdl" -message = "The following tokens are required: comma. (122:3)" - -[[concerns]] -kind = "ParseError" -document = "broadinstitute/warp:/pipelines/broad/dna_seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.wdl" -message = "The following tokens are required: comma. (126:5)" - -[[concerns]] -kind = "ParseError" -document = "broadinstitute/warp:/tasks/broad/Funcotator.wdl" -message = "The following tokens are required: whitespace, comment. (120:78)" - -[[concerns]] -kind = "ParseError" -document = "broadinstitute/warp:/tasks/broad/GermlineVariantDiscovery.wdl" -message = "The following tokens are required: string. (65:32)" +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" +message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:143:23: error: expected runtime key, but found `,`" + +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" +message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:174:29: error: expected runtime key, but found `,`" -[[concerns]] -kind = "ParseError" -document = "broadinstitute/warp:/tasks/broad/InternalTasks.wdl" -message = "The following tokens are required: whitespace, comment. (64:77)" +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" +message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:175:23: error: expected runtime key, but found `,`" -[[concerns]] -kind = "ParseError" -document = "broadinstitute/warp:/tasks/broad/SplitLargeReadGroup.wdl" -message = "The following tokens are required: comma. (48:5)" +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" +message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:210:29: error: expected runtime key, but found `,`" -[[concerns]] -kind = "ParseError" -document = "broadinstitute/warp:/tasks/broad/UltimaGenomicsWholeGenomeGermlineAlignmentMarkDuplicates.wdl" -message = "The following tokens are required: comma. (56:7)" +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" +message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:211:23: error: expected runtime key, but found `,`" -[[concerns]] -kind = "ParseError" -document = "broadinstitute/warp:/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl" -message = "The following tokens are required: string. (814:27)" +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" +message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:244:29: error: expected runtime key, but found `,`" -[[concerns]] -kind = "ParseError" -document = "broadinstitute/warp:/tasks/skylab/FastqProcessing.wdl" -message = "The following tokens are not allowed: space. (162:12)" +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" +message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:245:23: error: expected runtime key, but found `,`" -[[concerns]] -kind = "ParseError" -document = "broadinstitute/warp:/tests/cemba/pr/CheckCembaOutputs.wdl" -message = "The following tokens are required: document. (1:1)" - -[[concerns]] -kind = "ParseError" -document = "broadinstitute/warp:/verification/VerifyTasks.wdl" -message = "The following tokens are required: or, and, add, sub, mul, div, remainder, eq, neq, lte, gte, lt, gt. (75:119)" - -[[concerns]] -kind = "ParseError" -document = "stjudecloud/workflows:/template/task-templates.wdl" -message = "The following tokens are required: expression. (49:35)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/freyja/wf_freyja_dashboard.wdl" -message = "The following tokens are required: workflow_call_input. (26:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/freyja/wf_freyja_fastq.wdl" -message = "The following tokens are required: workflow_call_input. (49:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/freyja/wf_freyja_plot.wdl" -message = "The following tokens are required: workflow_call_input. (22:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/freyja/wf_freyja_update.wdl" -message = "The following tokens are required: workflow_call_input. (12:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/phylogenetics/wf_augur.wdl" -message = "The following tokens are required: workflow_call_input. (49:5)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/phylogenetics/wf_augur_prep.wdl" -message = "The following tokens are required: workflow_call_input. (30:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/phylogenetics/wf_core_gene_snp.wdl" -message = "The following tokens are required: workflow_call_input. (90:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/phylogenetics/wf_find_shared_variants.wdl" -message = "The following tokens are required: workflow_call_input. (29:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/phylogenetics/wf_ksnp3.wdl" -message = "The following tokens are required: workflow_call_input. (72:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/phylogenetics/wf_lyveset.wdl" -message = "The following tokens are required: workflow_call_input. (24:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/phylogenetics/wf_mashtree_fasta.wdl" -message = "The following tokens are required: workflow_call_input. (44:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/phylogenetics/wf_nextclade_addToRefTree.wdl" -message = "The following tokens are required: workflow_call_input. (31:5)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/phylogenetics/wf_snippy_streamline.wdl" -message = "The following tokens are required: workflow_call_input. (56:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/phylogenetics/wf_snippy_tree.wdl" -message = "The following tokens are required: workflow_call_input. (186:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/standalone_modules/wf_amrfinderplus.wdl" -message = "The following tokens are required: workflow_call_input. (18:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/standalone_modules/wf_gambit_query.wdl" -message = "The following tokens are required: workflow_call_input. (18:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/standalone_modules/wf_gambitcore.wdl" -message = "The following tokens are required: workflow_call_input. (18:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/standalone_modules/wf_kraken2_ont.wdl" -message = "The following tokens are required: workflow_call_input. (29:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/standalone_modules/wf_kraken2_pe.wdl" -message = "The following tokens are required: workflow_call_input. (31:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/standalone_modules/wf_kraken2_se.wdl" -message = "The following tokens are required: workflow_call_input. (29:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/standalone_modules/wf_rasusa.wdl" -message = "The following tokens are required: workflow_call_input. (24:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/standalone_modules/wf_snippy_variants.wdl" -message = "The following tokens are required: workflow_call_input. (56:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/standalone_modules/wf_tbprofiler_tngs.wdl" -message = "The following tokens are required: workflow_call_input. (20:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/submission/wf_terra_2_ncbi.wdl" -message = "The following tokens are required: workflow_call_input. (23:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/theiacov/updates/wf_ncbi_scrub_pe.wdl" -message = "The following tokens are required: workflow_call_input. (27:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/theiacov/updates/wf_ncbi_scrub_se.wdl" -message = "The following tokens are required: workflow_call_input. (24:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/theiacov/updates/wf_pangolin_update.wdl" -message = "The following tokens are required: workflow_call_input. (61:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/theiacov/updates/wf_vadr_update.wdl" -message = "The following tokens are required: workflow_call_input. (20:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/theiacov/wf_theiacov_clearlabs.wdl" -message = "The following tokens are required: workflow_call_input. (161:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/theiacov/wf_theiacov_fasta.wdl" -message = "The following tokens are required: workflow_call_input. (120:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/theiacov/wf_theiacov_fasta_batch.wdl" -message = "The following tokens are required: workflow_call_input. (62:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/theiacov/wf_theiacov_illumina_pe.wdl" -message = "The following tokens are required: workflow_call_input. (344:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/theiacov/wf_theiacov_illumina_se.wdl" -message = "The following tokens are required: workflow_call_input. (204:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/theiacov/wf_theiacov_ont.wdl" -message = "The following tokens are required: workflow_call_input. (346:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/theiaeuk/wf_cauris_cladetyper.wdl" -message = "The following tokens are required: workflow_call_input. (18:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/theiaeuk/wf_theiaeuk_illumina_pe.wdl" -message = "The following tokens are required: workflow_call_input. (50:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/theiameta/wf_theiameta_illumina_pe.wdl" -message = "The following tokens are required: workflow_call_input. (180:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/theiaprok/wf_theiaprok_fasta.wdl" -message = "The following tokens are required: workflow_call_input. (52:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl" -message = "The following tokens are required: workflow_call_input. (69:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/theiaprok/wf_theiaprok_illumina_se.wdl" -message = "The following tokens are required: workflow_call_input. (69:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/theiaprok/wf_theiaprok_ont.wdl" -message = "The following tokens are required: workflow_call_input. (65:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/utilities/data_import/wf_assembly_fetch.wdl" -message = "The following tokens are required: workflow_call_input. (27:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/utilities/data_import/wf_basespace_fetch.wdl" -message = "The following tokens are required: workflow_call_input. (26:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/utilities/file_handling/wf_concatenate_column.wdl" -message = "The following tokens are required: workflow_call_input. (18:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/utilities/file_handling/wf_rename_fastq_files.wdl" -message = "The following tokens are required: workflow_call_input. (29:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/utilities/file_handling/wf_transfer_column.wdl" -message = "The following tokens are required: workflow_call_input. (18:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/utilities/file_handling/wf_zip_column.wdl" -message = "The following tokens are required: workflow_call_input. (18:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/utilities/wf_czgenepi_prep.wdl" -message = "The following tokens are required: workflow_call_input. (37:3)" - -[[concerns]] -kind = "ParseError" -document = "theiagen/public_health_bioinformatics:/workflows/utilities/wf_theiavalidate.wdl" -message = "The following tokens are required: workflow_call_input. (54:3)" - -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" +message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:284:29: error: expected runtime key, but found `,`" + +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" +message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:285:23: error: expected runtime key, but found `,`" + +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" +message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:323:29: error: expected runtime key, but found `,`" + +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" +message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:324:23: error: expected runtime key, but found `,`" + +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" +message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:325:28: error: expected runtime key, but found `,`" + +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" +message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:326:48: error: expected runtime key, but found `,`" + +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl" +message = "/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl:58:29: error: expected runtime key, but found `,`" + +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl" +message = "/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl:59:23: error: expected runtime key, but found `,`" + +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl" +message = "/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl:83:29: error: expected runtime key, but found `,`" + +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl" +message = "/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl:84:23: error: expected runtime key, but found `,`" + +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl" +message = "/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl:85:28: error: expected runtime key, but found `,`" + +[[diagnostics]] +document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl" +message = "/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl:86:48: error: expected runtime key, but found `,`" + +[[diagnostics]] document = "biowdl/tasks:/bcftools.wdl" -message = '''[v1::E001] invalid escape character: '\_' (114:75-114:77)''' +message = '/bcftools.wdl:114:75: error: unknown escape sequence `\_`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/bedtools.wdl" -message = '''[v1::E001] invalid escape character: '\.' (27:48-27:50)''' +message = '/bedtools.wdl:27:48: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/bowtie.wdl" -message = '''[v1::E001] invalid escape character: '\.' (63:32-63:34)''' +message = '/bowtie.wdl:63:32: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/bowtie.wdl" -message = '''[v1::E001] invalid escape character: '\.' (63:39-63:41)''' +message = '/bowtie.wdl:63:39: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/bowtie.wdl" -message = '''[v1::E001] invalid escape character: '\.' (63:46-63:48)''' +message = '/bowtie.wdl:63:46: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/bowtie.wdl" -message = '''[v1::E001] invalid escape character: '\.' (75:48-75:50)''' +message = '/bowtie.wdl:75:48: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/centrifuge.wdl" -message = '''[v1::E001] invalid escape character: '\.' (122:57-122:59)''' +message = '/centrifuge.wdl:122:57: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/centrifuge.wdl" -message = '''[v1::E001] invalid escape character: '\.' (122:64-122:66)''' +message = '/centrifuge.wdl:122:64: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/centrifuge.wdl" -message = '''[v1::E001] invalid escape character: '\.' (199:57-199:59)''' +message = '/centrifuge.wdl:199:57: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/centrifuge.wdl" -message = '''[v1::E001] invalid escape character: '\.' (199:64-199:66)''' +message = '/centrifuge.wdl:199:64: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/centrifuge.wdl" -message = '''[v1::E001] invalid escape character: '\.' (256:57-256:59)''' +message = '/centrifuge.wdl:256:57: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/centrifuge.wdl" -message = '''[v1::E001] invalid escape character: '\.' (256:64-256:66)''' +message = '/centrifuge.wdl:256:64: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/common.wdl" -message = '''[v1::E001] invalid escape character: '\.' (275:45-275:47)''' +message = '/common.wdl:275:45: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/fastqc.wdl" -message = '''[v1::E001] invalid escape character: '\.' (59:42-59:44)''' +message = '/fastqc.wdl:59:42: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/fastqc.wdl" -message = '''[v1::E001] invalid escape character: '\.' (63:54-63:56)''' +message = '/fastqc.wdl:63:54: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/fastqc.wdl" -message = '''[v1::E001] invalid escape character: '\.' (63:58-63:60)''' +message = '/fastqc.wdl:63:58: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/gatk.wdl" -message = '''[v1::E001] invalid escape character: '\.' (127:57-127:59)''' +message = '/gatk.wdl:127:57: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/gatk.wdl" -message = '''[v1::E001] invalid escape character: '\.' (1597:41-1597:43)''' +message = '/gatk.wdl:1597:41: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/hisat2.wdl" -message = '''[v1::E001] invalid escape character: '\.' (60:34-60:36)''' +message = '/hisat2.wdl:60:34: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/hisat2.wdl" -message = '''[v1::E001] invalid escape character: '\.' (60:41-60:43)''' +message = '/hisat2.wdl:60:41: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/multiqc.wdl" -message = '''[v1::E001] invalid escape character: '\.' (133:45-133:47)''' +message = '/multiqc.wdl:133:45: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/picard.wdl" -message = '''[v1::E001] invalid escape character: '\.' (1021:48-1021:50)''' +message = '/picard.wdl:1021:48: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/picard.wdl" -message = '''[v1::E001] invalid escape character: '\.' (1191:48-1191:50)''' +message = '/picard.wdl:1191:48: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/picard.wdl" -message = '''[v1::E001] invalid escape character: '\.' (643:51-643:53)''' +message = '/picard.wdl:643:51: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/picard.wdl" -message = '''[v1::E001] invalid escape character: '\.' (785:51-785:53)''' +message = '/picard.wdl:785:51: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/picard.wdl" -message = '''[v1::E001] invalid escape character: '\.' (900:46-900:48)''' +message = '/picard.wdl:900:46: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/picard.wdl" -message = '''[v1::E001] invalid escape character: '\.' (901:46-901:48)''' +message = '/picard.wdl:901:46: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/picard.wdl" -message = '''[v1::E001] invalid escape character: '\.' (902:49-902:51)''' +message = '/picard.wdl:902:49: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/sambamba.wdl" -message = '''[v1::E001] invalid escape character: '\.' (145:49-145:51)''' +message = '/sambamba.wdl:145:49: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/sambamba.wdl" -message = '''[v1::E001] invalid escape character: '\.' (157:60-157:62)''' +message = '/sambamba.wdl:157:60: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/sambamba.wdl" -message = '''[v1::E001] invalid escape character: '\.' (91:44-91:46)''' +message = '/sambamba.wdl:91:44: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/samtools.wdl" -message = '''[v1::E001] invalid escape character: '\.' (238:53-238:55)''' +message = '/samtools.wdl:238:53: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/samtools.wdl" -message = '''[v1::E001] invalid escape character: '\.' (326:44-326:46)''' +message = '/samtools.wdl:326:44: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/samtools.wdl" -message = '''[v1::E001] invalid escape character: '\.' (414:44-414:46)''' +message = '/samtools.wdl:414:44: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/samtools.wdl" -message = '''[v1::E001] invalid escape character: '\.' (458:49-458:51)''' +message = '/samtools.wdl:458:49: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/samtools.wdl" -message = '''[v1::E001] invalid escape character: '\.' (470:60-470:62)''' +message = '/samtools.wdl:470:60: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/samtools.wdl" -message = '''[v1::E001] invalid escape character: '\.' (80:42-80:44)''' +message = '/samtools.wdl:80:42: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/umi-tools.wdl" -message = '''[v1::E001] invalid escape character: '\.' (95:49-95:51)''' +message = '/umi-tools.wdl:95:49: error: unknown escape sequence `\.`' -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "biowdl/tasks:/umi.wdl" -message = '''[v1::E001] invalid escape character: '\.' (39:60-39:62)''' +message = '/umi.wdl:39:60: error: unknown escape sequence `\.`' + +[[diagnostics]] +document = "broadinstitute/palantir-workflows:/HaplotypeMap/BuildHaplotypeMap.wdl" +message = "/HaplotypeMap/BuildHaplotypeMap.wdl:17:1: error: a WDL document must start with a version statement" -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "broadinstitute/warp:/pipelines/skylab/scATAC/scATAC.wdl" -message = "[v1::E003] duplicate runtime keys: 'cpu' (199:9-199:12, 203:9-203:12)" +message = "/pipelines/skylab/scATAC/scATAC.wdl:203:9: error: duplicate key `cpu` in runtime section" + +[[diagnostics]] +document = "broadinstitute/warp:/tasks/broad/GermlineVariantDiscovery.wdl" +message = "/tasks/broad/GermlineVariantDiscovery.wdl:137:32: error: expected string, but found integer" + +[[diagnostics]] +document = "broadinstitute/warp:/tasks/broad/GermlineVariantDiscovery.wdl" +message = "/tasks/broad/GermlineVariantDiscovery.wdl:65:32: error: expected string, but found integer" + +[[diagnostics]] +document = "broadinstitute/warp:/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl" +message = "/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl:814:27: error: expected string, but found integer" + +[[diagnostics]] +document = "broadinstitute/warp:/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl" +message = "/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl:866:27: error: expected string, but found integer" + +[[diagnostics]] +document = "broadinstitute/warp:/tests/cemba/pr/CheckCembaOutputs.wdl" +message = "/tests/cemba/pr/CheckCembaOutputs.wdl:1:1: error: a WDL document must start with a version statement" -[[concerns]] -kind = "ValidationFailure" +[[diagnostics]] document = "chanzuckerberg/czid-workflows:/workflows/index-generation/index-generation.wdl" -message = "[v1::E002] invalid version: 'version development' (1:1-1:20)" +message = "/workflows/index-generation/index-generation.wdl:1:9: error: unsupported WDL version `development`" diff --git a/wdl-gauntlet/CHANGELOG.md b/wdl-gauntlet/CHANGELOG.md index 8c34f22ba..d402f5878 100644 --- a/wdl-gauntlet/CHANGELOG.md +++ b/wdl-gauntlet/CHANGELOG.md @@ -5,6 +5,12 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## Unreleased + +### Changed + +* Migrated `wdl-gauntlet` to use the new parser implementation ([#76](https://github.com/stjude-rust-labs/wdl/pull/76)) + ## 0.2.0 - 5-31-2024 ### Changed diff --git a/wdl-gauntlet/Cargo.toml b/wdl-gauntlet/Cargo.toml index bbeb85d26..5e1f37e0e 100644 --- a/wdl-gauntlet/Cargo.toml +++ b/wdl-gauntlet/Cargo.toml @@ -8,20 +8,20 @@ edition.workspace = true # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html [dependencies] +wdl-ast = { path = "../wdl-ast", version = "0.2.0", features = ["codespan"] } +wdl-lint = { path = "../wdl-lint", version = "0.3.0" } clap.workspace = true colored.workspace = true -dirs = "5.0.1" +dirs.workspace = true env_logger.workspace = true -faster-hex = "0.9.0" -git2 = "0.18.3" +faster-hex.workspace = true +git2.workspace = true indexmap.workspace = true log.workspace = true -nonempty.workspace = true serde.workspace = true serde_with.workspace = true -temp-dir = "0.1.13" +temp-dir.workspace = true tokio.workspace = true toml.workspace = true -wdl-ast = { path = "../wdl-ast", version = "0.2.0" } -wdl-core = { path = "../wdl-core", version = "0.2.0" } -wdl-grammar = { path = "../wdl-grammar", version = "0.3.0" } +anyhow.workspace = true +codespan-reporting.workspace = true diff --git a/wdl-gauntlet/src/config.rs b/wdl-gauntlet/src/config.rs index f819ad415..badeea56d 100644 --- a/wdl-gauntlet/src/config.rs +++ b/wdl-gauntlet/src/config.rs @@ -7,13 +7,10 @@ use std::path::PathBuf; use log::debug; use log::log_enabled; use log::trace; -use wdl_core::Version; pub mod inner; -pub mod reportable_concern; pub use inner::Inner; -pub use reportable_concern::ReportableConcern; /// The default directory name for the `wdl-gauntlet` configuration file const DEFAULT_CONFIG_DIR: &str = "wdl-gauntlet"; @@ -117,8 +114,8 @@ impl Config { /// /// In both cases, the `path` will be stored within the [`Config`]. This has /// the effect of ensuring the value loaded here will be saved to the - /// inteded location (should [`Config::save()`] be called). - pub fn load_or_new(path: PathBuf, version: Version) -> Result { + /// intended location (should [`Config::save()`] be called). + pub fn load_or_new(path: PathBuf) -> Result { if !path.exists() { debug!( "no configuration exists at {}, creating new configuration.", @@ -126,7 +123,7 @@ impl Config { ); return Ok(Self { path: Some(path), - inner: Inner::from(version), + inner: Inner::default(), }); } @@ -143,63 +140,21 @@ impl Config { if log_enabled!(log::Level::Trace) { trace!("Loaded configuration file with the following:"); trace!(" -> {} repositories.", result.inner().repositories().len()); - let num_concerns = result.inner().concerns().len(); - trace!(" -> {} ignored errors.", num_concerns); + trace!( + " -> {} ignored diagnostics.", + result.inner().diagnostics().len() + ); } Ok(result) } /// Gets the [`Inner`] configuration by reference. - /// - /// ``` - /// use wdl_gauntlet as gauntlet; - /// - /// let config = r#"version = "v1" - /// - /// [repositories."Foo/Bar"] - /// identifier = "Foo/Bar""# - /// .parse::()?; - /// - /// assert_eq!(config.inner().version(), &wdl_core::Version::V1); - /// assert_eq!(config.inner().repositories().len(), 1); - /// assert_eq!(config.inner().concerns().len(), 0); - /// - /// Ok::<(), Box>(()) - /// ``` pub fn inner(&self) -> &Inner { &self.inner } /// Gets the [`Inner`] configuration by mutable reference. - /// - /// ``` - /// use indexmap::IndexSet; - /// use wdl_gauntlet as gauntlet; - /// use wdl_gauntlet::config::reportable_concern::Kind; - /// use wdl_gauntlet::config::ReportableConcern; - /// - /// let mut config = r#"version = "v1" - /// - /// [repositories."Foo/Bar"] - /// identifier = "Foo/Bar" - /// commit_hash = "d8e8b48ce8faad50b24779d785cd504baadfb13f""# - /// .parse::()?; - /// - /// let mut concerns = IndexSet::new(); - /// concerns.insert(ReportableConcern::new( - /// Kind::ValidationFailure, - /// "Foo/Bar:quux.wdl", - /// "Hello, world!", - /// )); - /// config.inner_mut().set_concerns(concerns); - /// - /// assert_eq!(config.inner().version(), &wdl_core::Version::V1); - /// assert_eq!(config.inner().repositories().len(), 1); - /// assert_eq!(config.inner().concerns().len(), 1); - /// - /// Ok::<(), Box>(()) - /// ``` pub fn inner_mut(&mut self) -> &mut Inner { &mut self.inner } diff --git a/wdl-gauntlet/src/config/inner.rs b/wdl-gauntlet/src/config/inner.rs index b34b73218..1a2216510 100644 --- a/wdl-gauntlet/src/config/inner.rs +++ b/wdl-gauntlet/src/config/inner.rs @@ -5,64 +5,76 @@ use std::path::Path; use indexmap::IndexMap; -use indexmap::IndexSet; use serde::Deserialize; use serde::Serialize; use serde_with::serde_as; -use crate::config::ReportableConcern; use crate::repository; -mod repr; +/// Represents a diagnostic reported for a document. +#[derive(Debug, Clone, Deserialize, Serialize, PartialEq, Eq, PartialOrd, Ord)] +pub struct Diagnostic { + /// The identifier of the document containing the diagnostic. + document: String, + /// The short-form diagnostic message. + message: String, +} + +impl Diagnostic { + /// Creates a new diagnostic for the given document identifier and message. + pub fn new(document: String, message: String) -> Self { + Self { document, message } + } -pub use repr::ReportableConcernsRepr; + /// Gets the identifier of the document. + pub fn document(&self) -> &str { + &self.document + } -/// A set of concerns serialized into their string form for storage within a -/// configuration file. -pub type ReportableConcerns = IndexSet; + /// Gets the diagnostic message. + pub fn message(&self) -> &str { + &self.message + } +} -/// The configuration object for a [`Config`](super::Config). +/// The configuration object for a [`Config`](super::Config). /// /// This object stores the actual configuration values for this subcommand. #[serde_as] #[derive(Debug, Default, Deserialize, Serialize)] pub struct Inner { - /// The WDL version. - version: wdl_core::Version, - /// The repositories. #[serde(default)] repositories: IndexMap, - /// The reportable concerns. - #[serde_as(as = "ReportableConcernsRepr")] - #[serde(default, skip_serializing_if = "IndexSet::is_empty")] - concerns: ReportableConcerns, + /// The expected diagnostics across all repositories. + #[serde(default)] + diagnostics: Vec, } impl Inner { - /// Gets the [`Version`](wdl_core::Version) for this [`Inner`] by reference. - /// - /// # Examples - /// - /// ``` - /// use gauntlet::config::Inner; - /// use wdl_gauntlet as gauntlet; - /// - /// let config = r#"version = "v1""#; - /// - /// let inner: Inner = toml::from_str(&config).unwrap(); - /// assert_eq!(inner.version(), &wdl_core::Version::V1); - /// ``` - pub fn version(&self) -> &wdl_core::Version { - &self.version - } - - /// Gets the [`Repositories`] for this [`Inner`] by reference. + /// Gets the repositories for this [`Inner`] by reference. pub fn repositories(&self) -> &IndexMap { &self.repositories } + /// Gets the list of expected diagnostics. + pub fn diagnostics(&self) -> &[Diagnostic] { + &self.diagnostics + } + + /// Sets the list of expected diagnostics. + pub fn set_diagnostics(&mut self, diagnostics: Vec) { + self.diagnostics = diagnostics; + } + + /// Gets the repositories for this [`Inner`] by mutable reference. + pub fn repositories_mut( + &mut self, + ) -> &mut IndexMap { + &mut self.repositories + } + /// Extends the `repositories` for this [`Inner`] with the given items. pub fn extend_repositories( &mut self, @@ -79,30 +91,12 @@ impl Inner { } } - /// Gets the [`ReportableConcerns`] for this [`Inner`] by reference. - pub fn concerns(&self) -> &ReportableConcerns { - &self.concerns - } - - /// Replaces the [`ReportableConcerns`] for this [`Inner`]. - pub fn set_concerns(&mut self, concerns: ReportableConcerns) { - self.concerns = concerns; - self.concerns.sort(); - } - - /// Sorts the [`Repositories`] and the [`ReportableConcerns`] by key. + /// Sorts the configuration. + /// + /// This sorts the repositories by their identifiers and the diagnostics by + /// their document identifiers and messages (lexicographically). pub fn sort(&mut self) { self.repositories.sort_by(|a, _, b, _| a.cmp(b)); - self.concerns.sort(); - } -} - -impl From for Inner { - fn from(version: wdl_core::Version) -> Self { - Self { - version, - repositories: Default::default(), - concerns: Default::default(), - } + self.diagnostics.sort(); } } diff --git a/wdl-gauntlet/src/config/inner/repr.rs b/wdl-gauntlet/src/config/inner/repr.rs deleted file mode 100644 index a6864ee02..000000000 --- a/wdl-gauntlet/src/config/inner/repr.rs +++ /dev/null @@ -1,29 +0,0 @@ -//! Representation of ignored errors as stored in the configuration file. - -// This compiler attribute is added because `serde_with` generates a struct -// below that does not have any documentation. The only way to silence the -// warning is to allow missing docs for this file. -#![allow(missing_docs)] - -use std::convert::Infallible; - -use crate::config::inner::ReportableConcerns; -use crate::config::ReportableConcern; - -serde_with::serde_conv!( - pub ReportableConcernsRepr, - ReportableConcerns, - |concerns: &ReportableConcerns| { - let mut result = concerns - .clone() - .into_iter() - .collect::>(); - result.sort(); - result - }, - |errors: Vec| -> Result<_, Infallible> { - Ok(errors - .into_iter() - .collect::()) - } -); diff --git a/wdl-gauntlet/src/config/reportable_concern.rs b/wdl-gauntlet/src/config/reportable_concern.rs deleted file mode 100644 index 1f05c4067..000000000 --- a/wdl-gauntlet/src/config/reportable_concern.rs +++ /dev/null @@ -1,197 +0,0 @@ -//! A reportable concern. -//! -//! Reportable concerns are [`Concern`](wdl_core::Concern)s that have been -//! simplified and serialized for reporting within a [configuration -//! file](crate::config::Inner). Reportable concerns ignore `LintWarning`s, -//! only focusing on `ParseError`s and `ValidationFailure`s. - -use serde::Deserialize; -use serde::Serialize; - -/// A kind of reportable concern. -#[derive(Clone, Debug, Deserialize, Eq, Hash, Ord, PartialEq, PartialOrd, Serialize)] -pub enum Kind { - /// A parse error. - ParseError, - - /// A validation failure. - ValidationFailure, - - /// A lint warning. - LintWarning, -} - -/// A representation of an error to ignore as serialized in the configuration -/// file. -/// -/// In short, I wanted to convert the -/// [`Concerns`](crate::config::inner::ReportableConcerns) object to something -/// more visually understandable in the configuration file. Thus, the only -/// purpose of this struct is to serialize and deserialize entries in that -/// [`HashMap`](std::collections::HashMap) in a prettier way. -#[derive(Clone, Debug, Deserialize, Eq, Hash, Ord, PartialEq, PartialOrd, Serialize)] -pub struct ReportableConcern { - /// The kind. - kind: Kind, - - /// The document containing the concern. - document: String, - - /// The concern message. - message: String, -} - -impl ReportableConcern { - /// Create a new [`ReportableConcern`]. - /// - /// **Note:** most often, you'll use [`ReportableConcern::from_concern()`] - /// to convert a [`Concern`](wdl_core::Concern) to a [`ReportableConcern`]. - /// - /// # Examples - /// - /// ``` - /// use wdl_gauntlet::config::reportable_concern::Kind; - /// use wdl_gauntlet::config::ReportableConcern; - /// - /// let reportable_concern = - /// ReportableConcern::new(Kind::ValidationFailure, "Foo/Bar:quux.wdl", "Hello, world!"); - /// - /// assert_eq!(reportable_concern.kind(), &Kind::ValidationFailure); - /// assert_eq!(reportable_concern.document(), "Foo/Bar:quux.wdl"); - /// assert_eq!(reportable_concern.message(), "Hello, world!"); - /// ``` - pub fn new(kind: Kind, document: impl Into, message: impl Into) -> Self { - let document = document.into(); - let message = message.into(); - - Self { - kind, - document, - message, - } - } - - /// Create a new [`ReportableConcern`] from a document name and a - /// [`Concern`](wdl_core::Concern). - /// - /// # Examples - /// - /// ``` - /// use wdl_core::concern::parse; - /// use wdl_core::file::Location; - /// use wdl_core::Concern; - /// use wdl_gauntlet::config::reportable_concern::Kind; - /// use wdl_gauntlet::config::ReportableConcern; - /// - /// let error = parse::Error::new("Hello, world!", Location::Unplaced); - /// let concern = Concern::ParseError(error); - /// - /// let reportable_concern = - /// ReportableConcern::from_concern("Foo/Bar:quux.wdl", concern, false).unwrap(); - /// - /// assert_eq!(reportable_concern.message(), "Hello, world!"); - /// assert_eq!(reportable_concern.document(), "Foo/Bar:quux.wdl"); - /// assert_eq!(reportable_concern.kind(), &Kind::ParseError); - /// ``` - pub fn from_concern( - document: impl Into, - concern: wdl_core::Concern, - arena: bool, - ) -> Option { - let document = document.into(); - let message = concern.to_string(); - - match &concern { - wdl_core::Concern::LintWarning(_) => { - if !arena { - None - } else { - Some(ReportableConcern { - kind: Kind::LintWarning, - document, - message, - }) - } - } - wdl_core::Concern::ParseError(_) => { - if arena { - None - } else { - Some(ReportableConcern { - kind: Kind::ParseError, - document, - message, - }) - } - } - wdl_core::Concern::ValidationFailure(_) => { - if arena { - None - } else { - Some(ReportableConcern { - kind: Kind::ValidationFailure, - document, - message, - }) - } - } - } - } - - /// Gets the [`Kind`] from the [`ReportableConcern`] by reference. - /// - /// # Examples - /// - /// ``` - /// use wdl_gauntlet::config::reportable_concern::Kind; - /// use wdl_gauntlet::config::ReportableConcern; - /// - /// let reportable_concern = - /// ReportableConcern::new(Kind::ValidationFailure, "Foo/Bar:quux.wdl", "Hello, world!"); - /// - /// assert_eq!(reportable_concern.kind(), &Kind::ValidationFailure); - /// ``` - pub fn kind(&self) -> &Kind { - &self.kind - } - - /// Gets the document name from the [`ReportableConcern`] by reference. - /// - /// # Examples - /// - /// ``` - /// use wdl_gauntlet::config::reportable_concern::Kind; - /// use wdl_gauntlet::config::ReportableConcern; - /// - /// let reportable_concern = - /// ReportableConcern::new(Kind::ValidationFailure, "Foo/Bar:quux.wdl", "Hello, world!"); - /// - /// assert_eq!(reportable_concern.document(), "Foo/Bar:quux.wdl"); - /// ``` - pub fn document(&self) -> &str { - self.document.as_ref() - } - - /// Gets the concern message from the [`ReportableConcern`] by reference. - /// - /// # Examples - /// - /// ``` - /// use wdl_gauntlet::config::reportable_concern::Kind; - /// use wdl_gauntlet::config::ReportableConcern; - /// - /// let reportable_concern = - /// ReportableConcern::new(Kind::ValidationFailure, "Foo/Bar:quux.wdl", "Hello, world!"); - /// - /// assert_eq!(reportable_concern.message(), "Hello, world!"); - /// ``` - pub fn message(&self) -> &str { - self.message.as_ref() - } -} - -impl std::fmt::Display for ReportableConcern { - fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { - write!(f, "|{}| {}", self.document, self.message) - } -} diff --git a/wdl-gauntlet/src/document/identifier.rs b/wdl-gauntlet/src/document/identifier.rs index 37cf1ea7c..94198d14d 100644 --- a/wdl-gauntlet/src/document/identifier.rs +++ b/wdl-gauntlet/src/document/identifier.rs @@ -78,6 +78,11 @@ impl Identifier { pub fn repository(&self) -> &repository::Identifier { &self.repository } + + /// Gets the path of the document. + pub fn path(&self) -> &str { + &self.path + } } impl std::fmt::Display for Identifier { diff --git a/wdl-gauntlet/src/lib.rs b/wdl-gauntlet/src/lib.rs index 60cb39401..e89e2afec 100644 --- a/wdl-gauntlet/src/lib.rs +++ b/wdl-gauntlet/src/lib.rs @@ -8,15 +8,23 @@ use std::path::PathBuf; use std::process; +use std::time::Duration; +use std::time::Instant; +use anyhow::Context; +use anyhow::Result; use clap::Parser; -use colored::Colorize as _; +use codespan_reporting::files::SimpleFile; +use codespan_reporting::term; +use codespan_reporting::term::termcolor::Buffer; +use codespan_reporting::term::termcolor::ColorChoice; +use codespan_reporting::term::termcolor::StandardStream; +use codespan_reporting::term::DisplayStyle; +use colored::Colorize; use indexmap::IndexSet; use log::debug; use log::info; use log::trace; -use wdl_ast as ast; -use wdl_grammar as grammar; pub mod config; pub mod document; @@ -25,56 +33,20 @@ pub mod repository; pub use config::Config; pub use report::Report; +use report::Status; +use report::UnmatchedStatus; pub use repository::Repository; +use wdl_ast::experimental::Document; +use wdl_ast::experimental::Validator; +use wdl_lint::v1::rules; -use crate::config::ReportableConcern; -use crate::report::Status; -use crate::repository::Identifier; use crate::repository::WorkDir; /// The exit code to emit when any test unexpectedly fails. -const EXIT_CODE_FAILED: i32 = 1; +const EXIT_CODE_UNEXPECTED: i32 = 1; /// The exit code to emit when an error was expected but not encountered. -const EXIT_CODE_UNDETECTED_IGNORED_CONCERNS: i32 = 2; - -/// An error related to the `wdl-grammar gauntlet` subcommand. -#[derive(Debug)] -pub enum Error { - /// A WDL 1.x abstract syntax tree error. - AstV1(ast::v1::Error), - - /// A configuration file error. - Config(config::Error), - - /// An input/output error. - Io(std::io::Error), - - /// A WDL 1.x parse tree error. - GrammarV1(grammar::v1::Error), - - /// An error related to a repository [`Identifier`]. - RepositoryIdentifier(repository::identifier::Error), -} - -impl std::fmt::Display for Error { - fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { - match self { - Error::AstV1(err) => write!(f, "ast error: {err}"), - Error::Config(err) => write!(f, "configuration file error: {err}"), - Error::Io(err) => write!(f, "i/o error: {err}"), - Error::GrammarV1(err) => write!(f, "grammar error: {err}"), - Error::RepositoryIdentifier(err) => { - write!(f, "repository identifier error: {err}") - } - } - } -} - -impl std::error::Error for Error {} - -/// A [`Result`](std::result::Result) with an [`Error`]. -type Result = std::result::Result; +const EXIT_CODE_MISSING: i32 = 2; /// A command-line utility for testing the compatibility of `wdl-grammar` and /// `wdl-ast` against a wide variety of community WDL repositories. @@ -86,9 +58,9 @@ pub struct Args { /// test repository specified on the CL. Normally, there is only one /// repository on disk at a time. The difference in disk space usage /// should be negligible. - pub repositories: Option>, + pub repositories: Vec, - /// Enable "arena mode", which switches the reported concerns from + /// Enable "arena mode", which switches the reported diagnostics from /// syntax errors to opinionated lint warnings. #[arg(short, long)] pub arena: bool, @@ -104,8 +76,8 @@ pub struct Args { /// If provided, only shows tests whose identifier contains the provided /// string(s). - #[arg(short, long)] - pub filter: Option>, + #[arg(short, long = "filter")] + pub filters: Vec, /// Enables logging for all modules (not just `wdl-gauntlet`). #[arg(short, long)] @@ -123,7 +95,7 @@ pub struct Args { #[arg(short, long)] pub quiet: bool, - /// Overwrites the configuration file with new expected concerns and the + /// Overwrites the configuration file with new expected diagnostics and the /// latest commit hashes. This will create temporary shallow clones of every /// test repository. Normally, there is only one repository on disk at a /// time. The difference in disk space usage should be negligible. @@ -134,10 +106,6 @@ pub struct Args { #[arg(long)] pub show_warnings: bool, - /// The Workflow Description Language (WDL) specification version to use. - #[arg(value_name = "VERSION", long, default_value_t, value_enum)] - pub specification_version: wdl_core::Version, - /// All available information, including trace information, is logged in /// the console. #[arg(short, long)] @@ -157,7 +125,7 @@ pub async fn gauntlet(args: Args) -> Result<()> { } false => { let path = args.config_file.unwrap_or(Config::default_path(args.arena)); - Config::load_or_new(path, args.specification_version).map_err(Error::Config)? + Config::load_or_new(path)? } }; @@ -168,47 +136,38 @@ pub async fn gauntlet(args: Args) -> Result<()> { config.inner_mut().update_repositories(work_dir.root()); } - if let Some(repositories) = args.repositories { - repositories.into_iter().for_each(|value| { - let identifier = value - .parse::() - .map_err(Error::RepositoryIdentifier) - .unwrap(); - work_dir.add_by_identifier(&identifier); - }); - config - .inner_mut() - .extend_repositories(work_dir.repositories().clone()) + for repo in args.repositories.into_iter() { + let identifier = repo + .parse() + .with_context(|| format!("repository identifier `{repo}` is not valid"))?; + work_dir.add_by_identifier(&identifier); } - let mut report = Report::from(std::io::stdout().lock()); + config + .inner_mut() + .extend_repositories(work_dir.repositories().clone()); + let mut report = Report::from(StandardStream::stdout(ColorChoice::Auto)); + let mut total_time = Duration::ZERO; for (index, (repository_identifier, repo)) in config.inner().repositories().iter().enumerate() { - let results = repo.wdl_files(work_dir.root()); - - report.title(repository_identifier).map_err(Error::Io)?; - report.next_section().map_err(Error::Io)?; - - for (relative_path, content) in results { + let files = repo.wdl_files(work_dir.root()); + report.title(repository_identifier).with_context(|| { + format!("failed to write report title for repository `{repository_identifier}`") + })?; + report + .next_section() + .context("failed to write next section")?; + + for (relative_path, source) in files { let abs_path = work_dir .root() .join(repository_identifier.organization()) .join(repository_identifier.name()) .join(&relative_path); - if let Some(ref filters) = args.filter { - let mut skip = true; - for filter in filters { - if content.contains(filter) { - skip = false; - break; - } - } - - if skip { - trace!("skipping: {:?}", abs_path); - continue; - } + if args.filters.contains(&relative_path) || repo.filters().contains(&relative_path) { + trace!("skipping: {:?}", abs_path); + continue; } trace!("processing: {:?}", abs_path); @@ -216,166 +175,177 @@ pub async fn gauntlet(args: Args) -> Result<()> { let document_identifier = document::Identifier::new(repository_identifier.clone(), relative_path); - match config.inner().version() { - wdl_core::Version::V1 => { - let mut detected_concerns = IndexSet::new(); - - let (pt, these_concerns) = grammar::v1::parse(&content) - .map_err(Error::GrammarV1)? - .into_parts(); - if let Some(these_concerns) = these_concerns { - detected_concerns.extend(these_concerns.into_inner().iter().filter_map( - |concern| { - // from_concern() will return `None` if the concern is not - // of the right type (based on the value of `args.arena`) - // in which case filter_map() will drop it. - ReportableConcern::from_concern( - document_identifier.to_string(), - concern.clone(), - args.arena, - ) - }, - )); + // Parse and validate the document + // If "arena mode" is activated, also validate with the lint rules enabled + let before = Instant::now(); + let diagnostics = match Document::parse(&source).into_result() { + Ok(document) => { + let mut validator = Validator::default(); + if args.arena { + validator.add_v1_visitors(rules().into_iter().map(|r| r.visitor())); } - if let Some(pt) = pt { - let (_, these_concerns) = - ast::v1::parse(pt).map_err(Error::AstV1)?.into_parts(); - if let Some(these_concerns) = these_concerns { - detected_concerns.extend( - these_concerns.into_inner().iter().filter_map(|concern| { - // from_concern() will return `None` if the concern is not - // of the right type (based on the value of `args.arena`) - // in which case filter_map() will drop it. - ReportableConcern::from_concern( - document_identifier.to_string(), - concern.clone(), - args.arena, - ) - }), - ); + match validator.validate(&document) { + Ok(()) => None, + Err(diagnostics) => Some(diagnostics), + } + } + Err(diagnostics) => Some(diagnostics), + }; + let elapsed = before.elapsed(); + total_time += elapsed; + + // Convert the diagnostics to a set of short-form messages + let mut actual = IndexSet::new(); + if let Some(diagnostics) = diagnostics { + let file: SimpleFile<_, _> = SimpleFile::new(document_identifier.path(), source); + let config = codespan_reporting::term::Config { + display_style: DisplayStyle::Short, + ..Default::default() + }; + + for diagnostic in diagnostics.iter() { + let mut buffer = Buffer::no_color(); + term::emit(&mut buffer, &config, &file, &diagnostic.to_codespan()) + .context("failed to write diagnostic")?; + + assert!( + actual.insert( + std::str::from_utf8(buffer.as_slice()) + .context("diagnostic should be UTF-8")? + .trim() + .to_string() + ) + ); + } + } + + // As the list of diagnostics has been sorted by document identifier, do + // a binary search and collect the matching messages + let diagnostics = config.inner().diagnostics(); + let doc_id_str = document_identifier.to_string(); + let expected: IndexSet = diagnostics + .binary_search_by_key(&doc_id_str.as_str(), |d| d.document()) + .map(|mut start_index| { + // As binary search may return any matching index, back up until we find the + // start of the range + for i in (0..start_index).rev() { + if diagnostics[i].document() != doc_id_str { + break; } + + start_index -= 1; } - let expected_concerns = config - .inner() - .concerns() + diagnostics[start_index..] .iter() - .filter_map(|concern| { - if concern.document() == document_identifier.to_string() { - Some(concern.clone()) + .map_while(|d| { + if d.document() == doc_id_str { + Some(d.message().to_string()) } else { None } }) - .collect::>(); - - let unexpected_concerns = &detected_concerns - &expected_concerns; - let missing_concerns = &expected_concerns - &detected_concerns; - - if !unexpected_concerns.is_empty() { - report - .register( - document_identifier, - Status::UnexpectedConcerns( - unexpected_concerns.into_iter().collect::>(), - ), - ) - .map_err(Error::Io)?; - } else if !missing_concerns.is_empty() { - report - .register( - document_identifier, - Status::MissingExpectedConcerns( - missing_concerns.into_iter().collect::>(), - ), - ) - .map_err(Error::Io)?; - } else if !detected_concerns.is_empty() { - report - .register(document_identifier, Status::ConcernsMatched) - .map_err(Error::Io)?; - } else { - report - .register(document_identifier, Status::Success) - .map_err(Error::Io)?; + .collect() + }) + .unwrap_or_default(); + + let unexpected = &actual - &expected; + let missing = &expected - &actual; + + let status = if !unexpected.is_empty() || !missing.is_empty() { + Status::DiagnosticsUnmatched( + UnmatchedStatus { + missing, + unexpected, + all: actual, } - } - } + .into(), + ) + } else if !actual.is_empty() { + Status::DiagnosticsMatched(actual) + } else { + Status::Success + }; + + report + .register(document_identifier, status, elapsed) + .context("failed to register report status")?; } - report.next_section().map_err(Error::Io)?; + report + .next_section() + .context("failed to transition to next report section")?; if !args.no_errors { report .report_unexpected_errors(repository_identifier) - .map_err(Error::Io)?; + .context("failed to report unexpected errors")?; } - report.next_section().map_err(Error::Io)?; - - report.footer(repository_identifier).map_err(Error::Io)?; - report.next_section().map_err(Error::Io)?; + report + .next_section() + .context("failed to transition to next report section")?; + report + .footer(repository_identifier) + .context("failed to write report footer")?; + report + .next_section() + .context("failed to transition to next report section")?; if index != config.inner().repositories().len() - 1 { println!(); } } - let missing_but_expected = report - .results() - .clone() - .into_iter() - .filter_map(|(_, status)| match status { - Status::MissingExpectedConcerns(concerns) => Some(concerns), - _ => None, - }) - .flatten() - .collect::>(); - - let unexpected = report - .results() - .clone() - .into_iter() - .filter_map(|(_, status)| match status { - Status::UnexpectedConcerns(concerns) => Some(concerns), - _ => None, - }) - .flatten() - .collect::>(); + let mut missing = 0; + let mut unexpected = 0; + let mut diagnostics = Vec::new(); + for (identifier, status) in report.into_results() { + let messages = match status { + Status::Success => continue, + Status::DiagnosticsMatched(all) => all, + Status::DiagnosticsUnmatched(unmatched) => { + missing += unmatched.missing.len(); + unexpected += unmatched.unexpected.len(); + unmatched.all + } + }; - if args.refresh { - info!("adding {} new expected concerns.", unexpected.len()); - info!( - "removing {} outdated expected concerns.", - missing_but_expected.len() - ); + // Don't bother rebuilding the diagnostics + if !args.refresh { + continue; + } + + for message in messages { + diagnostics.push(config::inner::Diagnostic::new( + identifier.to_string(), + message, + )); + } + } + + println!("\nTotal analysis time: {total_time:?}"); - let existing = config.inner().concerns().clone(); - let new = existing - .difference(&missing_but_expected) - .chain(unexpected.iter()) - .cloned() - .collect::>(); - config.inner_mut().set_concerns(new); + if args.refresh { + info!("adding {unexpected} new expected diagnostics."); + info!("removing {missing} outdated expected diagnostics."); - config.save().map_err(Error::Config)?; - } else if !missing_but_expected.is_empty() { + config.inner_mut().set_diagnostics(diagnostics); + config.inner_mut().sort(); + config.save().context("failed to save configuration file")?; + } else if missing > 0 { println!( "\n{}\n", - "undetected but expected concerns remain: you should remove these from your \ + "missing but expected diagnostics remain: you should remove these from your \ configuration file or run the command with the `--refresh` option!" .red() .bold() ); - for concern in missing_but_expected { - println!("{}\n\n", concern); - } - - process::exit(EXIT_CODE_UNDETECTED_IGNORED_CONCERNS); - } else if !unexpected.is_empty() { - process::exit(EXIT_CODE_FAILED); + process::exit(EXIT_CODE_MISSING); + } else if unexpected > 0 { + process::exit(EXIT_CODE_UNEXPECTED); } Ok(()) diff --git a/wdl-gauntlet/src/report.rs b/wdl-gauntlet/src/report.rs index cedba9638..0b4fcb3d2 100644 --- a/wdl-gauntlet/src/report.rs +++ b/wdl-gauntlet/src/report.rs @@ -1,40 +1,46 @@ //! Reporting. use std::collections::HashMap; +use std::time::Duration; use colored::Colorize as _; -use indexmap::IndexMap; +use indexmap::IndexSet; -use crate::config::ReportableConcern; use crate::document; use crate::repository; +/// Represents an unmatched status. +#[derive(Clone, Debug)] +pub struct UnmatchedStatus { + /// The missing set of diagnostics. + /// + /// These are the diagnostics that were in the config but were not + /// emitted by the parser/validator. + pub missing: IndexSet, + /// The unexpected set of diagnostics. + /// + /// These are the diagnostics that were not in the configuration but + /// were emitted by the parser/validator. + pub unexpected: IndexSet, + /// The set of all diagnostics that were emitted. + pub all: IndexSet, +} + /// The status of a single parsing test. -#[derive(Clone, Debug, Eq, Hash, PartialEq)] +#[derive(Clone, Debug)] pub enum Status { /// The document passed parsing, validation, and linting successfully with - /// no concerns for both the parse tree and the abstract syntax tree. + /// no diagnostics to report. Success, - /// The document had concerns, but the concerns exactly matched what was - /// already expected in the configuration, meaning that this [`Status`] is - /// considered successful. - ConcernsMatched, - - /// The document had concerns, and some concerns were missing from what was - /// expected in the configuration. This [`Status`] is considered a test - /// failure. - UnexpectedConcerns(Vec), + /// The document had diagnostics, but the diagnostics exactly matched what + /// was already expected in the configuration, meaning that this + /// [`Status`] is considered successful. + DiagnosticsMatched(IndexSet), - /// The document had concerns, and all of those concerns were accounted for - /// in the configuration. However, there were some concerns declared in the - /// configuration that were not found. This [`Status`] is considered a test - /// failure. - /// - /// Note: this represents a situation where a concern was removed from the - /// source document. In this case, the concern likely needs to be removed - /// from the expected concerns. - MissingExpectedConcerns(Vec), + /// The document had diagnostics, but they did not match what was expected + /// in the configuration. + DiagnosticsUnmatched(Box), } /// A printable section within a report for a repository. @@ -46,8 +52,8 @@ pub enum Section { /// Summarized status of each parsing test. Summary, - /// Detailed information on unexpected concerns that were encountered. - Concerns, + /// Detailed information on unexpected diagnostics that were encountered. + Diagnostics, /// Summarized information about all results reported. Footer, @@ -60,10 +66,8 @@ impl Status { /// of tests that passed for a repository. pub fn success(&self) -> bool { match self { - Status::Success => true, - Status::ConcernsMatched => true, - Status::UnexpectedConcerns(_) => false, - Status::MissingExpectedConcerns(_) => false, + Self::Success | Self::DiagnosticsMatched(_) => true, + Self::DiagnosticsUnmatched { .. } => false, } } } @@ -71,10 +75,19 @@ impl Status { impl std::fmt::Display for Status { fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { match self { - Status::Success => write!(f, "✅"), - Status::ConcernsMatched => write!(f, "📘"), - Status::UnexpectedConcerns(_) => write!(f, "❌"), - Status::MissingExpectedConcerns(_) => write!(f, "🔄️"), + Self::Success => write!(f, "✅"), + Self::DiagnosticsMatched(_) => write!(f, "📘"), + Self::DiagnosticsUnmatched(status) => { + if !status.unexpected.is_empty() { + write!(f, "❌")?; + } + + if !status.missing.is_empty() { + write!(f, "🔄️")?; + } + + Ok(()) + } } } } @@ -108,12 +121,11 @@ pub struct Report { } impl Report { - /// Gets the [`Results`] for this [`Report`] by reference. - /// - /// **Note:** see the note at [Self::results] for a caveat on interpretation - /// of these results. - pub fn results(&self) -> &Results { - &self.results + /// Consumes the report and returns the [`Results`]. + // **Note:** see the note at [Self::results] for a caveat on interpretation + // of these results. + pub fn into_results(self) -> Results { + self.results } /// Transitions to the next section of the report. @@ -128,9 +140,9 @@ impl Report { write!(self.inner, "⚠️ No items reported for this repository!")?; } - Section::Concerns + Section::Diagnostics } - Section::Concerns => Section::Footer, + Section::Diagnostics => Section::Footer, Section::Footer => Section::Title, }; @@ -164,6 +176,7 @@ impl Report { &mut self, identifier: document::Identifier, status: Status, + elapsed: Duration, ) -> std::io::Result<()> { if self.section != Section::Summary { panic!( @@ -172,7 +185,7 @@ impl Report { ); } - writeln!(self.inner, "{} {}", status, identifier)?; + writeln!(self.inner, "{status} {identifier} ({elapsed:?})")?; self.results.insert(identifier, status); self.printed = true; @@ -184,26 +197,37 @@ impl Report { &mut self, repository_identifier: &repository::Identifier, ) -> std::io::Result<()> { - if self.section != Section::Concerns { + if self.section != Section::Diagnostics { panic!( - "cannot report unexpected concerns when the report phase is {:?}", + "cannot report unexpected diagnostics when the report phase is {:?}", self.section ); } - for (id, concerns) in self + for (i, (id, status)) in self .results .iter() .filter(|(id, _)| id.repository() == repository_identifier) .filter_map(|(id, status)| match status { - Status::MissingExpectedConcerns(concerns) => Some((id.to_string(), concerns)), - Status::UnexpectedConcerns(concerns) => Some((id.to_string(), concerns)), + Status::DiagnosticsUnmatched(status) => Some((id, status)), _ => None, }) + .enumerate() { - for concern in concerns { - writeln!(self.inner, "{}\n\n{}\n", id.italic(), concern)?; - self.printed = true; + self.printed = true; + + if i > 0 { + writeln!(self.inner)?; + } + + writeln!(self.inner, "{id}", id = id.path().italic())?; + + for diagnostic in &status.unexpected { + writeln!(self.inner, "❌ {diagnostic}")?; + } + + for diagnostic in &status.missing { + writeln!(self.inner, "🔄️ {diagnostic}")?; } } @@ -226,59 +250,41 @@ impl Report { return Ok(()); } - let test_results = self + let (passed, considered, missing, unexpected) = self .results .iter() - .filter(|(identifer, _)| identifer.repository() == repository_identifier) - .fold(IndexMap::::new(), |mut hm, (_, status)| { - *hm.entry(status.clone()).or_default() += 1; - hm - }); + .filter(|(id, _)| id.repository() == repository_identifier) + .map(|(_, s)| s) + .fold((0, 0, 0, 0), |mut counts, status| { + if status.success() { + counts.0 += 1 + } - let passed = test_results - .iter() - .filter(|(status, _)| status.success()) - .fold(0usize, |mut acc, (_, count)| { - acc += count; - acc - }); + counts.1 += 1; + + if let Status::DiagnosticsUnmatched(unmatched) = status { + counts.2 += unmatched.missing.len(); + counts.3 += unmatched.unexpected.len(); + } - let considered = test_results.iter().fold(0usize, |mut acc, (_, count)| { - acc += count; - acc - }); + counts + }); write!(self.inner, "Passed {}/{} tests", passed, considered)?; let mut with = Vec::new(); - match self - .results - .iter() - .flat_map(|(_, status)| match status { - Status::MissingExpectedConcerns(concerns) => Some(concerns.len()), - _ => None, - }) - .sum::() - { + match missing { 0 => {} - 1 => with.push(String::from("1 missing concern")), - v => with.push(format!("{} missing concerns", v)), - }; + 1 => with.push(String::from("1 missing diagnostic")), + v => with.push(format!("{} missing diagnostics", v)), + } - match self - .results - .iter() - .flat_map(|(_, status)| match status { - Status::UnexpectedConcerns(concerns) => Some(concerns.len()), - _ => None, - }) - .sum::() - { + match unexpected { 0 => {} - 1 => with.push(String::from("1 unexpected concern")), - v => with.push(format!("{} unexpected concerns", v)), - }; + 1 => with.push(String::from("1 unexpected diagnostic")), + v => with.push(format!("{} unexpected diagnostics", v)), + } if !with.is_empty() { write!(self.inner, " (with {})", with.join(" and "))?; diff --git a/wdl-gauntlet/src/repository.rs b/wdl-gauntlet/src/repository.rs index e23d8eea6..36bcddb9e 100644 --- a/wdl-gauntlet/src/repository.rs +++ b/wdl-gauntlet/src/repository.rs @@ -51,14 +51,18 @@ impl<'de> Deserialize<'de> for RawHash { } } -/// A repository of GitHub files. -#[derive(Clone, Eq, PartialEq, Hash, Serialize, Deserialize, Debug)] +/// A GitHub repository of WDL files. +#[derive(Debug, Clone, Serialize, Deserialize, Eq, PartialEq)] pub struct Repository { /// The name for the [`Repository`] expressed as an [`Identifier`]. identifier: Identifier, /// The commit hash for the [`Repository`]. commit_hash: Option, + + /// A list of documents that should be filtered out from the repository. + #[serde(default, skip_serializing_if = "Vec::is_empty")] + filters: Vec, } impl Repository { @@ -107,6 +111,7 @@ impl Repository { Self { identifier, commit_hash: Some(commit_hash), + filters: Default::default(), } } @@ -120,6 +125,11 @@ impl Repository { &self.commit_hash } + /// Gets the file path filters for the repository. + pub fn filters(&self) -> &[String] { + &self.filters + } + /// Retrieve all the WDL files from the [`Repository`]. pub fn wdl_files(&self, root: &Path) -> IndexMap { let repo_root = root @@ -217,12 +227,12 @@ impl Repository { /// Add to an [`IndexMap`] all the WDL files in a directory /// and its subdirectories. -fn add_wdl_files(path: &PathBuf, wdl_files: &mut IndexMap, leading_dirs: &Path) { +fn add_wdl_files(path: &PathBuf, wdl_files: &mut IndexMap, repo_root: &Path) { if path.is_dir() { for entry in std::fs::read_dir(path).expect("failed to read directory") { let entry = entry.expect("failed to read entry"); let path = entry.path(); - add_wdl_files(&path, wdl_files, leading_dirs); + add_wdl_files(&path, wdl_files, repo_root); } } else if path.is_file() { let path_str = path @@ -230,13 +240,14 @@ fn add_wdl_files(path: &PathBuf, wdl_files: &mut IndexMap, leadi .expect("failed to convert file name to string"); if path_str.ends_with(".wdl") { let contents = std::fs::read_to_string(path).expect("failed to read file contents"); - // Strip leading directories from the path. + // Strip the repo root from the path and normalize backslashes to slash. // SAFETY: `path_str` is guaranteed to start with `leading_dirs` wdl_files.insert( path_str - .strip_prefix(leading_dirs.to_str().unwrap()) - .unwrap() - .to_string(), + .strip_prefix(repo_root.to_str().expect("path should be UTF-8")) + .expect("path should start with repo root") + .to_string() + .replace('\\', "/"), contents, ); } diff --git a/wdl-lint/src/v1.rs b/wdl-lint/src/v1.rs index b6e544541..91310a925 100644 --- a/wdl-lint/src/v1.rs +++ b/wdl-lint/src/v1.rs @@ -1,7 +1,5 @@ //! Module for V1 lint rules. -use convert_case::Case; -use convert_case::Casing; use wdl_ast::experimental::v1::Visitor; use wdl_ast::experimental::Diagnostics; @@ -75,6 +73,8 @@ pub fn rules() -> Vec> { // Ensure all the rule ids are unique and pascal case #[cfg(debug_assertions)] { + use convert_case::Case; + use convert_case::Casing; let mut set = std::collections::HashSet::new(); for r in rules.iter() { if r.id().to_case(Case::Pascal) != r.id() { From 79d1b7f4b9792537f24c523c92a3a2de7857eccc Mon Sep 17 00:00:00 2001 From: Peter Huene Date: Wed, 12 Jun 2024 10:31:24 -0700 Subject: [PATCH 2/6] fix: remove `ENCODE-DCC/chip-seq-pipeline2` from arena. The `ENCODE-DCC/chip-seq-pipeline2` repo has too many lint rule violations to be useful to track in `Arena.toml`. This also skips over logging diagnostics for files that fail to parse when arena mode is turned on; this removes the duplicated diagnostics from `Arena.toml` and `Gauntlet.toml`. --- Arena.toml | 6968 --------------------------------------- wdl-gauntlet/src/lib.rs | 12 +- 2 files changed, 11 insertions(+), 6969 deletions(-) diff --git a/Arena.toml b/Arena.toml index 2952ca80d..412287685 100644 --- a/Arena.toml +++ b/Arena.toml @@ -1,7 +1,3 @@ -[repositories."ENCODE-DCC/chip-seq-pipeline2"] -identifier = "ENCODE-DCC/chip-seq-pipeline2" -commit_hash = "26eeda81a0540dc793fc69b0c390d232ca7ca50a" - [repositories."getwilds/ww-fastq-to-cram"] identifier = "getwilds/ww-fastq-to-cram" commit_hash = "7dd6c4c7c8c9fc6dcd4eb5ff8f3262cd26d5e7cc" @@ -11,6970 +7,6 @@ identifier = "stjudecloud/workflows" commit_hash = "a44b18a30fd6192af713fded4bc824f6e77f6ff9" filters = ["/template/task-templates.wdl"] -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1001:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1002:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1003:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1006:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1007:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1008:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1011:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1012:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1013:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1016:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1017:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1018:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:101:21: warning: input name `fastqs_rep1_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1021:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1022:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1023:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1027:27: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1027:55: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1027:9: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:102:21: warning: input name `fastqs_rep1_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1030:27: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1030:55: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1030:9: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1033:27: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1033:55: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1033:9: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:103:21: warning: input name `fastqs_rep2_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1043:10: warning: private declaration name `ref_fa_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1044:11: warning: private declaration name `bwa_idx_tar_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1046:10: warning: private declaration name `bowtie2_idx_tar_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1047:10: warning: private declaration name `chrsz_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1048:12: warning: private declaration name `gensz_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1049:11: warning: private declaration name `blacklist1_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:104:21: warning: input name `fastqs_rep2_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1051:11: warning: private declaration name `blacklist2_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:105:21: warning: input name `fastqs_rep3_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1064:11: warning: private declaration name `blacklist_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1067:12: warning: private declaration name `mito_chr_name_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1068:12: warning: private declaration name `regex_bfilt_peak_chr_name_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1069:12: warning: private declaration name `genome_name_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:106:21: warning: input name `fastqs_rep3_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1072:12: warning: private declaration name `aligner_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1072:56: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1073:12: warning: private declaration name `peak_caller_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1073:45: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1073:82: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1074:57: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1075:12: warning: private declaration name `peak_type_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1075:42: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1075:53: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1076:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1077:41: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1078:12: warning: private declaration name `idr_rank_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1078:41: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1078:52: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1079:47: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1079:60: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:107:21: warning: input name `fastqs_rep4_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1080:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1082:36: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1083:44: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1083:9: warning: private declaration name `cap_num_peak_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1085:9: warning: private declaration name `mapq_thresh_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1086:13: warning: private declaration name `enable_xcor_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1086:46: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1087:13: warning: private declaration name `enable_count_signal_track_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1087:60: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1088:13: warning: private declaration name `enable_jsd_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1088:45: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1089:13: warning: private declaration name `enable_gc_bias_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1089:49: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:108:21: warning: input name `fastqs_rep4_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1090:13: warning: private declaration name `align_only_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1090:45: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1092:11: warning: private declaration name `align_mem_factor_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1092:45: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1094:11: warning: private declaration name `align_disk_factor_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1094:46: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1096:11: warning: private declaration name `call_peak_mem_factor_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1096:53: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1098:11: warning: private declaration name `call_peak_disk_factor_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1098:54: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:109:21: warning: input name `fastqs_rep5_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:10:27: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1102:24: warning: private declaration name `fastqs_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1102:35: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:110:21: warning: input name `fastqs_rep5_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:111:21: warning: input name `fastqs_rep6_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:112:21: warning: input name `fastqs_rep6_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1130:24: warning: private declaration name `fastqs_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1130:35: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1135:24: warning: private declaration name `ctl_fastqs_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1135:39: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:113:21: warning: input name `fastqs_rep7_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:114:21: warning: input name `fastqs_rep7_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:115:21: warning: input name `fastqs_rep8_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1163:24: warning: private declaration name `ctl_fastqs_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1163:39: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:116:21: warning: input name `fastqs_rep8_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:117:21: warning: input name `fastqs_rep9_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:118:21: warning: input name `fastqs_rep9_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1193:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1197:42: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1199:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:119:21: warning: input name `fastqs_rep10_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1203:112: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1203:66: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1203:87: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1205:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1209:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:120:21: warning: input name `fastqs_rep10_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1211:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1215:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1217:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1221:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1223:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1230:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1231:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1232:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1233:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1234:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1235:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1239:27: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1241:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1245:27: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1247:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1256:17: warning: private declaration name `paired_end_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1272:39: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1273:38: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1289:15: warning: private declaration name `bam_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1315:15: warning: private declaration name `nodup_bam_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1333:15: warning: private declaration name `ta_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:133:21: warning: input name `ctl_fastqs_rep1_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:134:21: warning: input name `ctl_fastqs_rep1_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:135:21: warning: input name `ctl_fastqs_rep2_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:136:21: warning: input name `ctl_fastqs_rep2_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1379:39: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:137:21: warning: input name `ctl_fastqs_rep3_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1380:38: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:138:21: warning: input name `ctl_fastqs_rep3_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:139:21: warning: input name `ctl_fastqs_rep4_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:13:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:140:21: warning: input name `ctl_fastqs_rep4_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:141:21: warning: input name `ctl_fastqs_rep5_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:142:21: warning: input name `ctl_fastqs_rep5_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:143:21: warning: input name `ctl_fastqs_rep6_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:144:21: warning: input name `ctl_fastqs_rep6_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:145:21: warning: input name `ctl_fastqs_rep7_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:146:21: warning: input name `ctl_fastqs_rep7_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:147:21: warning: input name `ctl_fastqs_rep8_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:148:21: warning: input name `ctl_fastqs_rep8_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1493:14: warning: private declaration name `fraglen_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:149:21: warning: input name `ctl_fastqs_rep9_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1501:17: warning: private declaration name `ctl_paired_end_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:150:21: warning: input name `ctl_fastqs_rep9_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1517:39: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1518:38: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:151:21: warning: input name `ctl_fastqs_rep10_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:152:21: warning: input name `ctl_fastqs_rep10_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1534:15: warning: private declaration name `ctl_bam_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1560:15: warning: private declaration name `ctl_nodup_bam_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1578:15: warning: private declaration name `ctl_ta_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1587:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1598:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:15:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1609:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1620:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:167:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:16:16: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1729:58: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1730:45: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1734:15: warning: private declaration name `peak_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:174:49: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1769:1: warning: line contains only whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1774:58: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1775:45: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1779:15: warning: private declaration name `peak_pr1_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:177:29: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:17:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1803:58: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1804:45: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1808:15: warning: private declaration name `peak_pr2_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1861:54: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1862:41: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1866:11: warning: private declaration name `peak_pooled_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1867:35: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:18:23: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1906:54: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1907:41: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1911:11: warning: private declaration name `peak_ppr1_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1935:54: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1936:41: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1940:11: warning: private declaration name `peak_ppr2_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1948:15: warning: private declaration name `peak1_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1949:15: warning: private declaration name `peak2_` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1953:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1953:46: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1969:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1969:46: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1990:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1990:38: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:1990:58: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2009:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2009:38: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2009:58: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2029:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2046:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2066:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2079:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:20:33: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2167:21: warning: input name `fastqs_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2167:21: warning: task `align` is missing a parameter metadata key for input `fastqs_R1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2168:21: warning: input name `fastqs_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2168:21: warning: task `align` is missing a parameter metadata key for input `fastqs_R2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2169:15: warning: task `align` is missing a parameter metadata key for input `ref_fa` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2170:14: warning: task `align` is missing a parameter metadata key for input `trim_bp` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2171:13: warning: task `align` is missing a parameter metadata key for input `crop_length` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2172:13: warning: task `align` is missing a parameter metadata key for input `crop_length_tol` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2173:17: warning: task `align` is missing a parameter metadata key for input `trimmomatic_phred_score_format` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2175:16: warning: task `align` is missing a parameter metadata key for input `aligner` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2177:16: warning: task `align` is missing a parameter metadata key for input `mito_chr_name` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2178:14: warning: task `align` is missing a parameter metadata key for input `multimapping` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2179:15: warning: task `align` is missing a parameter metadata key for input `custom_align_py` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2180:15: warning: task `align` is missing a parameter metadata key for input `idx_tar` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2181:17: warning: task `align` is missing a parameter metadata key for input `paired_end` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2182:17: warning: task `align` is missing a parameter metadata key for input `use_bwa_mem_for_pe` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2183:13: warning: task `align` is missing a parameter metadata key for input `bwa_mem_read_len_limit` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2184:17: warning: task `align` is missing a parameter metadata key for input `use_bowtie2_local_mode` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2186:17: warning: task `align` is missing a parameter metadata key for input `trimmomatic_java_heap` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2187:13: warning: task `align` is missing a parameter metadata key for input `cpu` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2188:15: warning: task `align` is missing a parameter metadata key for input `mem_factor` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2189:13: warning: task `align` is missing a parameter metadata key for input `time_hr` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2190:15: warning: task `align` is missing a parameter metadata key for input `disk_factor` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2192:28: warning: task `align` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2202:5: warning: task `align` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2213:34: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2213:54: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2214:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2237:38: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2237:75: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2238:38: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2238:58: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2241:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2243:38: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2243:72: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2244:162: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2244:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2245:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2253:38: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2253:66: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2254:38: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2254:58: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2255:46: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2255:74: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2256:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2257:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2258:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2264:38: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2264:66: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2265:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2266:38: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2266:58: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2267:50: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2267:65: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2268:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2269:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2274:38: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2274:66: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2275:38: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2275:58: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2276:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2277:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2282:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2283:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2284:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2288:25: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2289:25: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2290:32: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2291:34: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2295:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2297:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:22:25: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2308:15: warning: task `filter` is missing a parameter metadata key for input `bam` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2309:17: warning: task `filter` is missing a parameter metadata key for input `paired_end` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2310:15: warning: task `filter` is missing a parameter metadata key for input `ref_fa` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2311:17: warning: task `filter` is missing a parameter metadata key for input `redact_nodup_bam` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2312:16: warning: task `filter` is missing a parameter metadata key for input `dup_marker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2314:13: warning: task `filter` is missing a parameter metadata key for input `mapq_thresh` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2315:23: warning: task `filter` is missing a parameter metadata key for input `filter_chrs` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2316:14: warning: task `filter` is missing a parameter metadata key for input `chrsz` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2317:17: warning: task `filter` is missing a parameter metadata key for input `no_dup_removal` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2318:16: warning: task `filter` is missing a parameter metadata key for input `mito_chr_name` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2320:13: warning: task `filter` is missing a parameter metadata key for input `cpu` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2321:15: warning: task `filter` is missing a parameter metadata key for input `mem_factor` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2322:17: warning: task `filter` is missing a parameter metadata key for input `picard_java_heap` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2323:13: warning: task `filter` is missing a parameter metadata key for input `time_hr` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2324:15: warning: task `filter` is missing a parameter metadata key for input `disk_factor` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2326:28: warning: task `filter` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2334:5: warning: task `filter` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2338:34: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2338:54: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2340:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2341:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2342:33: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2343:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2344:38: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2344:62: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2345:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2346:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2347:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2348:138: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2348:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2353:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2358:31: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2359:31: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2360:32: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2361:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2362:39: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2366:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2368:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2378:15: warning: task `bam2ta` is missing a parameter metadata key for input `bam` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2379:17: warning: task `bam2ta` is missing a parameter metadata key for input `paired_end` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2380:16: warning: task `bam2ta` is missing a parameter metadata key for input `mito_chr_name` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2381:13: warning: task `bam2ta` is missing a parameter metadata key for input `subsample` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2383:13: warning: task `bam2ta` is missing a parameter metadata key for input `cpu` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2384:15: warning: task `bam2ta` is missing a parameter metadata key for input `mem_factor` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2385:13: warning: task `bam2ta` is missing a parameter metadata key for input `time_hr` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2386:15: warning: task `bam2ta` is missing a parameter metadata key for input `disk_factor` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2388:28: warning: task `bam2ta` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2395:5: warning: task `bam2ta` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:23:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2400:34: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2400:54: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2401:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2402:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2403:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2404:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2407:24: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2411:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2413:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2423:15: warning: task `spr` is missing a parameter metadata key for input `ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2424:17: warning: task `spr` is missing a parameter metadata key for input `paired_end` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2425:13: warning: task `spr` is missing a parameter metadata key for input `pseudoreplication_random_seed` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2427:15: warning: task `spr` is missing a parameter metadata key for input `mem_factor` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2428:15: warning: task `spr` is missing a parameter metadata key for input `disk_factor` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2430:28: warning: task `spr` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2436:5: warning: task `spr` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2440:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2441:34: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2441:54: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2444:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2445:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2449:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2451:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2461:22: warning: task `pool_ta` is missing a parameter metadata key for input `tas` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2462:14: warning: task `pool_ta` is missing a parameter metadata key for input `col` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2463:17: warning: task `pool_ta` is missing a parameter metadata key for input `prefix` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2465:28: warning: task `pool_ta` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2468:5: warning: task `pool_ta` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2471:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2472:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2473:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2476:31: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2480:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2482:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2492:15: warning: task `xcor` is missing a parameter metadata key for input `ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2493:17: warning: task `xcor` is missing a parameter metadata key for input `paired_end` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2494:16: warning: task `xcor` is missing a parameter metadata key for input `mito_chr_name` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2495:13: warning: task `xcor` is missing a parameter metadata key for input `subsample` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2498:17: warning: task `xcor` is missing a parameter metadata key for input `chip_seq_type` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2499:14: warning: task `xcor` is missing a parameter metadata key for input `exclusion_range_min` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:24:23: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2500:14: warning: task `xcor` is missing a parameter metadata key for input `exclusion_range_max` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2502:13: warning: task `xcor` is missing a parameter metadata key for input `cpu` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2503:15: warning: task `xcor` is missing a parameter metadata key for input `mem_factor` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2503:25: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2504:13: warning: task `xcor` is missing a parameter metadata key for input `time_hr` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2505:15: warning: task `xcor` is missing a parameter metadata key for input `disk_factor` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2507:28: warning: task `xcor` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2513:5: warning: task `xcor` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2517:34: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2517:54: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2518:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2519:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2520:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2521:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2522:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2523:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2524:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2527:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2528:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2529:27: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:252:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2530:33: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2535:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2537:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:253:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2547:22: warning: task `jsd` is missing a parameter metadata key for input `nodup_bams` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2548:22: warning: task `jsd` is missing a parameter metadata key for input `ctl_bams` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2549:15: warning: task `jsd` is missing a parameter metadata key for input `blacklist` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:254:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2550:13: warning: task `jsd` is missing a parameter metadata key for input `mapq_thresh` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2552:13: warning: task `jsd` is missing a parameter metadata key for input `cpu` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2553:15: warning: task `jsd` is missing a parameter metadata key for input `mem_factor` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2554:13: warning: task `jsd` is missing a parameter metadata key for input `time_hr` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2555:15: warning: task `jsd` is missing a parameter metadata key for input `disk_factor` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2557:28: warning: task `jsd` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2563:5: warning: task `jsd` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2566:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2567:42: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2567:84: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2568:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2569:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2570:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2573:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2574:36: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2578:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:257:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2580:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:258:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2590:22: warning: task `choose_ctl` is missing a parameter metadata key for input `tas` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2591:22: warning: task `choose_ctl` is missing a parameter metadata key for input `ctl_tas` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2592:15: warning: task `choose_ctl` is missing a parameter metadata key for input `ta_pooled` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2593:15: warning: task `choose_ctl` is missing a parameter metadata key for input `ctl_ta_pooled` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2594:17: warning: task `choose_ctl` is missing a parameter metadata key for input `always_use_pooled_ctl` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2595:15: warning: task `choose_ctl` is missing a parameter metadata key for input `ctl_depth_ratio` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2597:13: warning: task `choose_ctl` is missing a parameter metadata key for input `ctl_depth_limit` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2598:15: warning: task `choose_ctl` is missing a parameter metadata key for input `exp_ctl_depth_ratio_limit` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:259:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2600:28: warning: task `choose_ctl` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2603:5: warning: task `choose_ctl` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2606:25: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2607:29: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2608:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2609:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2610:45: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2610:76: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2611:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2612:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2613:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2616:39: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2617:46: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2618:53: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2625:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2627:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:262:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2637:15: warning: task `count_signal_track` is missing a parameter metadata key for input `ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2638:14: warning: task `count_signal_track` is missing a parameter metadata key for input `chrsz` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:263:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2640:28: warning: task `count_signal_track` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2644:5: warning: task `count_signal_track` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2648:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2649:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:264:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2652:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2653:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2657:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2659:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2669:15: warning: task `subsample_ctl` is missing a parameter metadata key for input `ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2670:17: warning: task `subsample_ctl` is missing a parameter metadata key for input `paired_end` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2671:13: warning: task `subsample_ctl` is missing a parameter metadata key for input `subsample` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2673:15: warning: task `subsample_ctl` is missing a parameter metadata key for input `mem_factor` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2674:15: warning: task `subsample_ctl` is missing a parameter metadata key for input `disk_factor` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2676:28: warning: task `subsample_ctl` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:267:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2682:5: warning: task `subsample_ctl` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2685:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2686:34: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2686:54: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2689:35: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:268:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2693:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2695:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:269:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2705:16: warning: task `call_peak` is missing a parameter metadata key for input `peak_caller` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2706:16: warning: task `call_peak` is missing a parameter metadata key for input `peak_type` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2707:22: warning: task `call_peak` is missing a parameter metadata key for input `tas` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2708:13: warning: task `call_peak` is missing a parameter metadata key for input `fraglen` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2709:16: warning: task `call_peak` is missing a parameter metadata key for input `gensz` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2711:14: warning: task `call_peak` is missing a parameter metadata key for input `chrsz` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2712:13: warning: task `call_peak` is missing a parameter metadata key for input `cap_num_peak` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2713:15: warning: task `call_peak` is missing a parameter metadata key for input `pval_thresh` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2714:16: warning: task `call_peak` is missing a parameter metadata key for input `fdr_thresh` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2716:15: warning: task `call_peak` is missing a parameter metadata key for input `blacklist` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2717:17: warning: task `call_peak` is missing a parameter metadata key for input `regex_bfilt_peak_chr_name` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2719:13: warning: task `call_peak` is missing a parameter metadata key for input `cpu` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2719:16: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2720:15: warning: task `call_peak` is missing a parameter metadata key for input `mem_factor` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2721:13: warning: task `call_peak` is missing a parameter metadata key for input `time_hr` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2722:15: warning: task `call_peak` is missing a parameter metadata key for input `disk_factor` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2724:28: warning: task `call_peak` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:272:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2730:5: warning: task `call_peak` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2735:23: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2736:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2737:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2738:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2739:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:273:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2740:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2741:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2745:23: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2746:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2747:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2748:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2749:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:274:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2750:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2755:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2756:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2756:78: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2757:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2758:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2759:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2760:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2763:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2763:65: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2765:32: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2765:53: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2766:35: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2766:56: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2767:39: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2767:60: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2768:40: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2768:61: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2769:44: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2769:65: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2770:29: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2771:41: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2772:43: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2773:33: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2776:33: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2777:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2779:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:277:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2780:23: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:278:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2790:22: warning: task `macs2_signal_track` is missing a parameter metadata key for input `tas` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2791:13: warning: task `macs2_signal_track` is missing a parameter metadata key for input `fraglen` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2792:16: warning: task `macs2_signal_track` is missing a parameter metadata key for input `gensz` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2794:14: warning: task `macs2_signal_track` is missing a parameter metadata key for input `chrsz` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2795:15: warning: task `macs2_signal_track` is missing a parameter metadata key for input `pval_thresh` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2797:15: warning: task `macs2_signal_track` is missing a parameter metadata key for input `mem_factor` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2798:13: warning: task `macs2_signal_track` is missing a parameter metadata key for input `time_hr` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2799:15: warning: task `macs2_signal_track` is missing a parameter metadata key for input `disk_factor` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:279:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2801:28: warning: task `macs2_signal_track` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2807:5: warning: task `macs2_signal_track` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2810:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2811:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2812:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2813:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2814:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2815:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2818:29: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2819:27: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2823:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2825:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:282:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2836:16: warning: task `idr` is missing a parameter metadata key for input `prefix` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2837:15: warning: task `idr` is missing a parameter metadata key for input `peak1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2838:15: warning: task `idr` is missing a parameter metadata key for input `peak2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2839:15: warning: task `idr` is missing a parameter metadata key for input `peak_pooled` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:283:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2840:15: warning: task `idr` is missing a parameter metadata key for input `idr_thresh` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2841:15: warning: task `idr` is missing a parameter metadata key for input `blacklist` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2842:16: warning: task `idr` is missing a parameter metadata key for input `regex_bfilt_peak_chr_name` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2844:15: warning: task `idr` is missing a parameter metadata key for input `ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2845:14: warning: task `idr` is missing a parameter metadata key for input `fraglen` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2846:14: warning: task `idr` is missing a parameter metadata key for input `chrsz` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2847:16: warning: task `idr` is missing a parameter metadata key for input `peak_type` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2848:16: warning: task `idr` is missing a parameter metadata key for input `rank` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:284:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2850:28: warning: task `idr` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2853:5: warning: task `idr` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2855:31: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2855:39: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2859:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2860:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2861:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2863:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2864:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2865:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2866:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2866:78: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2867:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2870:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2870:69: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2871:36: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2871:57: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2872:39: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2872:60: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2873:43: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2873:64: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2874:44: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2874:65: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2875:48: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2875:69: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2876:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2877:44: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2878:29: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2879:49: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2879:75: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:287:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2883:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2885:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:288:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2890:6: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2895:16: warning: task `overlap` is missing a parameter metadata key for input `prefix` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2896:15: warning: task `overlap` is missing a parameter metadata key for input `peak1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2897:15: warning: task `overlap` is missing a parameter metadata key for input `peak2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2898:15: warning: task `overlap` is missing a parameter metadata key for input `peak_pooled` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2899:15: warning: task `overlap` is missing a parameter metadata key for input `blacklist` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:289:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:28:24: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2900:16: warning: task `overlap` is missing a parameter metadata key for input `regex_bfilt_peak_chr_name` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2902:15: warning: task `overlap` is missing a parameter metadata key for input `ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2903:14: warning: task `overlap` is missing a parameter metadata key for input `fraglen` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2904:14: warning: task `overlap` is missing a parameter metadata key for input `chrsz` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2905:16: warning: task `overlap` is missing a parameter metadata key for input `peak_type` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2907:28: warning: task `overlap` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:290:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2910:5: warning: task `overlap` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2912:31: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2912:39: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2916:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2917:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2918:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2919:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2920:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2922:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2922:78: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2923:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2926:34: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2926:73: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2927:40: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2927:61: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2928:43: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2928:64: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2929:47: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2929:68: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2930:48: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2930:69: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2931:52: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2931:73: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2932:49: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2932:75: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2936:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2938:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:293:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2943:6: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2948:16: warning: task `reproducibility` is missing a parameter metadata key for input `prefix` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2949:21: warning: task `reproducibility` is missing a parameter metadata key for input `peaks` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:294:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2953:21: warning: task `reproducibility` is missing a parameter metadata key for input `peaks_pr` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2954:15: warning: task `reproducibility` is missing a parameter metadata key for input `peak_ppr` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2955:16: warning: task `reproducibility` is missing a parameter metadata key for input `peak_type` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2956:14: warning: task `reproducibility` is missing a parameter metadata key for input `chrsz` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2958:28: warning: task `reproducibility` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2961:5: warning: task `reproducibility` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2964:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2965:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2966:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2968:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2969:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2972:34: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2973:37: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2974:41: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2975:42: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2976:46: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2977:39: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2978:42: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2979:46: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:297:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2980:47: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2981:51: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2982:40: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2984:41: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2985:43: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2986:33: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:298:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2990:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2992:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:2997:6: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:29:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3002:15: warning: task `gc_bias` is missing a parameter metadata key for input `nodup_bam` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3003:14: warning: task `gc_bias` is missing a parameter metadata key for input `ref_fa` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3005:17: warning: task `gc_bias` is missing a parameter metadata key for input `picard_java_heap` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3007:28: warning: task `gc_bias` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3014:5: warning: task `gc_bias` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3017:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3018:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3019:138: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3019:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:301:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3022:29: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3023:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3027:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3029:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:302:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3040:16: warning: task `qc_report` is missing a parameter metadata key for input `pipeline_ver` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3041:16: warning: task `qc_report` is missing a parameter metadata key for input `title` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3042:16: warning: task `qc_report` is missing a parameter metadata key for input `description` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3043:17: warning: task `qc_report` is missing a parameter metadata key for input `genome` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3046:24: warning: task `qc_report` is missing a parameter metadata key for input `paired_ends` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3047:24: warning: task `qc_report` is missing a parameter metadata key for input `ctl_paired_ends` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3048:16: warning: task `qc_report` is missing a parameter metadata key for input `pipeline_type` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3049:16: warning: task `qc_report` is missing a parameter metadata key for input `aligner` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3050:17: warning: task `qc_report` is missing a parameter metadata key for input `no_dup_removal` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3051:16: warning: task `qc_report` is missing a parameter metadata key for input `peak_caller` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3052:13: warning: task `qc_report` is missing a parameter metadata key for input `cap_num_peak` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3053:15: warning: task `qc_report` is missing a parameter metadata key for input `idr_thresh` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3054:15: warning: task `qc_report` is missing a parameter metadata key for input `pval_thresh` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3055:13: warning: task `qc_report` is missing a parameter metadata key for input `xcor_trim_bp` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3056:13: warning: task `qc_report` is missing a parameter metadata key for input `xcor_subsample_reads` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3058:21: warning: task `qc_report` is missing a parameter metadata key for input `samstat_qcs` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3059:21: warning: task `qc_report` is missing a parameter metadata key for input `nodup_samstat_qcs` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:305:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3060:21: warning: task `qc_report` is missing a parameter metadata key for input `dup_qcs` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3061:21: warning: task `qc_report` is missing a parameter metadata key for input `lib_complexity_qcs` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3062:21: warning: task `qc_report` is missing a parameter metadata key for input `ctl_samstat_qcs` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3063:21: warning: task `qc_report` is missing a parameter metadata key for input `ctl_nodup_samstat_qcs` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3064:21: warning: task `qc_report` is missing a parameter metadata key for input `ctl_dup_qcs` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3065:21: warning: task `qc_report` is missing a parameter metadata key for input `ctl_lib_complexity_qcs` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3066:21: warning: task `qc_report` is missing a parameter metadata key for input `xcor_plots` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3067:21: warning: task `qc_report` is missing a parameter metadata key for input `xcor_scores` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3068:15: warning: task `qc_report` is missing a parameter metadata key for input `jsd_plot` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3069:21: warning: task `qc_report` is missing a parameter metadata key for input `jsd_qcs` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:306:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3070:21: warning: task `qc_report` is missing a parameter metadata key for input `idr_plots` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3071:21: warning: task `qc_report` is missing a parameter metadata key for input `idr_plots_pr` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3072:15: warning: task `qc_report` is missing a parameter metadata key for input `idr_plot_ppr` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3073:21: warning: task `qc_report` is missing a parameter metadata key for input `frip_qcs` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3074:21: warning: task `qc_report` is missing a parameter metadata key for input `frip_qcs_pr1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3075:21: warning: task `qc_report` is missing a parameter metadata key for input `frip_qcs_pr2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3076:15: warning: task `qc_report` is missing a parameter metadata key for input `frip_qc_pooled` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3077:15: warning: task `qc_report` is missing a parameter metadata key for input `frip_qc_ppr1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3077:27: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3078:15: warning: task `qc_report` is missing a parameter metadata key for input `frip_qc_ppr2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3078:27: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3079:21: warning: task `qc_report` is missing a parameter metadata key for input `frip_idr_qcs` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3080:21: warning: task `qc_report` is missing a parameter metadata key for input `frip_idr_qcs_pr` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3081:15: warning: task `qc_report` is missing a parameter metadata key for input `frip_idr_qc_ppr` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3081:30: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3082:21: warning: task `qc_report` is missing a parameter metadata key for input `frip_overlap_qcs` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3083:21: warning: task `qc_report` is missing a parameter metadata key for input `frip_overlap_qcs_pr` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3084:15: warning: task `qc_report` is missing a parameter metadata key for input `frip_overlap_qc_ppr` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3085:15: warning: task `qc_report` is missing a parameter metadata key for input `idr_reproducibility_qc` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3086:15: warning: task `qc_report` is missing a parameter metadata key for input `overlap_reproducibility_qc` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3088:21: warning: task `qc_report` is missing a parameter metadata key for input `gc_plots` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3090:21: warning: task `qc_report` is missing a parameter metadata key for input `peak_region_size_qcs` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3091:21: warning: task `qc_report` is missing a parameter metadata key for input `peak_region_size_plots` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3092:21: warning: task `qc_report` is missing a parameter metadata key for input `num_peak_qcs` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3094:15: warning: task `qc_report` is missing a parameter metadata key for input `idr_opt_peak_region_size_qc` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3095:15: warning: task `qc_report` is missing a parameter metadata key for input `idr_opt_peak_region_size_plot` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3096:15: warning: task `qc_report` is missing a parameter metadata key for input `idr_opt_num_peak_qc` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3098:15: warning: task `qc_report` is missing a parameter metadata key for input `overlap_opt_peak_region_size_qc` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3099:15: warning: task `qc_report` is missing a parameter metadata key for input `overlap_opt_peak_region_size_plot` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:309:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3100:15: warning: task `qc_report` is missing a parameter metadata key for input `overlap_opt_num_peak_qc` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3102:15: warning: task `qc_report` is missing a parameter metadata key for input `qc_json_ref` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3104:28: warning: task `qc_report` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3107:5: warning: task `qc_report` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:310:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3111:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3114:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3115:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3116:33: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3117:37: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3120:40: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3120:65: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3122:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3127:33: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3128:39: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3129:29: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3130:40: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3131:32: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3132:33: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3133:31: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3134:34: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3135:37: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3136:43: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3137:33: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3138:44: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3139:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:313:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3140:29: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3141:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3142:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3143:34: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3144:34: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3145:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3146:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3147:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3148:34: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3149:37: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:314:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3150:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3151:38: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3152:41: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3153:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3154:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3155:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3156:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3157:42: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3158:44: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3159:34: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:315:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3160:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3161:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3162:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3163:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3164:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3165:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3168:15: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3171:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3172:29: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3173:49: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3173:75: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3177:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3179:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3184:6: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:318:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3190:15: warning: task `read_genome_tsv` is missing a parameter metadata key for input `genome_tsv` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3191:17: warning: task `read_genome_tsv` is missing a parameter metadata key for input `null_s` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3193:28: warning: task `read_genome_tsv` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:319:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:320:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3214:43: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3215:34: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3215:76: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3216:39: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3216:86: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3217:43: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3217:94: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3218:33: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3218:74: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3219:33: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3219:74: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3220:37: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3220:82: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3221:38: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3221:84: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3222:41: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3222:90: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3223:53: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3223:90: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3224:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3229:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3231:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3231:36: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:323:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3241:20: warning: task `rounded_mean` is missing a parameter metadata key for input `ints` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3243:28: warning: task `rounded_mean` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3247:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:324:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3258:37: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:325:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3262:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3264:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3274:16: warning: task `raise_exception` is missing a parameter metadata key for input `msg` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3276:28: warning: task `raise_exception` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3278:5: warning: task `raise_exception` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3283:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3288:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:328:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:3290:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:329:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:32:24: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:330:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:333:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:334:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:337:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:338:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:339:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:33:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:343:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:344:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:345:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:348:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:349:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:350:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:352:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:356:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:357:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:358:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:360:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:364:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:365:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:366:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:368:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:36:24: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:372:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:373:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:374:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:376:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:37:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:380:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:381:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:382:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:385:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:386:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:387:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:38:23: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:390:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:391:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:392:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:395:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:396:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:397:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:400:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:401:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:402:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:405:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:406:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:407:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:410:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:411:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:412:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:415:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:416:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:417:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:41:24: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:420:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:421:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:422:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:425:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:426:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:427:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:42:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:430:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:431:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:432:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:435:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:436:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:437:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:43:23: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:440:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:441:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:442:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:445:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:446:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:447:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:450:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:451:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:452:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:455:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:456:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:457:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:460:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:461:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:462:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:465:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:466:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:467:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:46:24: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:470:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:471:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:472:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:475:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:476:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:477:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:47:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:480:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:481:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:482:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:485:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:486:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:487:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:48:23: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:490:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:491:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:492:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:495:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:496:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:497:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:500:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:501:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:502:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:506:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:507:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:508:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:511:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:512:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:513:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:516:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:517:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:518:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:51:24: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:520:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:524:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:525:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:526:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:528:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:52:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:532:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:533:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:534:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:536:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:53:23: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:540:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:541:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:542:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:544:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:548:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:549:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:550:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:553:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:554:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:555:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:558:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:559:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:560:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:563:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:564:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:565:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:568:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:569:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:56:24: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:570:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:573:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:574:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:575:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:578:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:579:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:57:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:580:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:583:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:584:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:585:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:588:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:589:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:58:23: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:590:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:593:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:594:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:595:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:598:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:599:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:600:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:603:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:604:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:605:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:608:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:609:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:610:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:613:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:614:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:615:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:618:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:619:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:61:24: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:620:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:623:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:624:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:625:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:628:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:629:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:62:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:630:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:633:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:634:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:635:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:638:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:639:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:63:23: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:640:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:644:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:645:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:646:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:647:23: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:647:29: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:647:40: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:648:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:651:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:652:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:653:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:656:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:657:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:658:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:661:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:662:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:663:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:666:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:667:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:66:24: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:670:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:671:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:674:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:675:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:679:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:67:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:680:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:681:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:682:23: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:682:34: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:682:41: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:683:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:686:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:687:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:688:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:68:23: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:691:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:692:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:693:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:696:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:697:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:698:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:701:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:702:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:703:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:706:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:707:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:708:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:711:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:712:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:713:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:716:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:717:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:718:23: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:718:31: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:718:42: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:719:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:722:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:723:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:724:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:727:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:728:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:729:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:732:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:733:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:734:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:735:23: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:735:33: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:736:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:739:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:740:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:741:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:744:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:745:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:746:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:749:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:74:25: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:750:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:751:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:754:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:755:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:756:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:759:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:75:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:760:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:761:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:764:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:765:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:766:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:769:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:76:24: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:770:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:771:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:774:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:775:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:776:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:779:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:77:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:780:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:781:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:784:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:785:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:786:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:789:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:78:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:790:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:791:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:794:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:795:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:796:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:799:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:800:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:801:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:802:22: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:805:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:806:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:807:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:810:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:811:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:812:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:816:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:817:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:818:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:81:24: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:821:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:822:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:823:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:826:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:827:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:828:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:82:30: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:831:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:832:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:836:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:837:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:838:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:841:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:842:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:843:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:846:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:847:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:848:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:851:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:852:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:853:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:856:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:857:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:858:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:861:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:862:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:863:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:866:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:867:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:868:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:871:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:872:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:873:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:876:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:877:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:878:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:881:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:882:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:883:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:886:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:887:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:888:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:88:15: warning: workflow `chip` is missing a parameter metadata key for input `bwa_idx_tar` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:891:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:892:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:893:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:896:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:897:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:898:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:901:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:902:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:903:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:906:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:907:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:908:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:911:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:912:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:913:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:916:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:917:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:918:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:921:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:922:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:923:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:926:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:927:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:928:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:931:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:932:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:933:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:936:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:937:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:938:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:941:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:942:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:943:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:946:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:947:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:948:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:951:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:952:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:953:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:956:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:957:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:958:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:961:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:962:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:963:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:966:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:967:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:968:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:971:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:972:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:973:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:976:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:977:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:978:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:981:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:982:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:983:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:986:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:987:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:988:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:991:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:992:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:993:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:996:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:997:20: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/chip.wdl" -message = "/chip.wdl:998:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/compare_md5sum.wdl" -message = "/dev/test/test_task/compare_md5sum.wdl:4:20: warning: task `compare_md5sum` is missing a parameter metadata key for input `labels` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/compare_md5sum.wdl" -message = "/dev/test/test_task/compare_md5sum.wdl:5:18: warning: task `compare_md5sum` is missing a parameter metadata key for input `files` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/compare_md5sum.wdl" -message = "/dev/test/test_task/compare_md5sum.wdl:6:18: warning: task `compare_md5sum` is missing a parameter metadata key for input `ref_files` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/compare_md5sum.wdl" -message = "/dev/test/test_task/compare_md5sum.wdl:84:45: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/compare_md5sum.wdl" -message = "/dev/test/test_task/compare_md5sum.wdl:85:46: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/compare_md5sum.wdl" -message = "/dev/test/test_task/compare_md5sum.wdl:86:26: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/compare_md5sum.wdl" -message = "/dev/test/test_task/compare_md5sum.wdl:87:39: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/compare_md5sum.wdl" -message = "/dev/test/test_task/compare_md5sum.wdl:91:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/compare_md5sum.wdl" -message = "/dev/test/test_task/compare_md5sum.wdl:93:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" -message = "/dev/test/test_task/test_bam2ta.wdl:10:16: warning: workflow `test_bam2ta` is missing a parameter metadata key for input `se_nodup_bam` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" -message = "/dev/test/test_task/test_bam2ta.wdl:12:16: warning: workflow `test_bam2ta` is missing a parameter metadata key for input `ref_pe_ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" -message = "/dev/test/test_task/test_bam2ta.wdl:13:16: warning: workflow `test_bam2ta` is missing a parameter metadata key for input `ref_pe_ta_subsample` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" -message = "/dev/test/test_task/test_bam2ta.wdl:14:16: warning: workflow `test_bam2ta` is missing a parameter metadata key for input `ref_se_ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" -message = "/dev/test/test_task/test_bam2ta.wdl:15:16: warning: workflow `test_bam2ta` is missing a parameter metadata key for input `ref_se_ta_subsample` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" -message = "/dev/test/test_task/test_bam2ta.wdl:16:16: warning: workflow `test_bam2ta` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" -message = "/dev/test/test_task/test_bam2ta.wdl:23:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" -message = "/dev/test/test_task/test_bam2ta.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" -message = "/dev/test/test_task/test_bam2ta.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" -message = "/dev/test/test_task/test_bam2ta.wdl:7:13: warning: workflow `test_bam2ta` is missing a parameter metadata key for input `bam2ta_subsample` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" -message = "/dev/test/test_task/test_bam2ta.wdl:81:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" -message = "/dev/test/test_task/test_bam2ta.wdl:82:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" -message = "/dev/test/test_task/test_bam2ta.wdl:83:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" -message = "/dev/test/test_task/test_bam2ta.wdl:84:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam2ta.wdl" -message = "/dev/test/test_task/test_bam2ta.wdl:9:16: warning: workflow `test_bam2ta` is missing a parameter metadata key for input `pe_nodup_bam` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:100:5: warning: task `samtools_flagstat` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:104:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:10:14: warning: workflow `test_bam_to_pbam` is missing a parameter metadata key for input `ref_fa` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:111:1: warning: missing newline at the end of the file [rule: EndingNewline]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:11:14: warning: workflow `test_bam_to_pbam` is missing a parameter metadata key for input `pe_bam` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:12:14: warning: workflow `test_bam_to_pbam` is missing a parameter metadata key for input `se_bam` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:14:14: warning: workflow `test_bam_to_pbam` is missing a parameter metadata key for input `chrsz` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:16:14: warning: workflow `test_bam_to_pbam` is missing a parameter metadata key for input `ref_pe_samtools_flagstat_qc` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:17:14: warning: workflow `test_bam_to_pbam` is missing a parameter metadata key for input `ref_se_samtools_flagstat_qc` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:18:16: warning: workflow `test_bam_to_pbam` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:25:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:46:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:65:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:7:16: warning: workflow `test_bam_to_pbam` is missing a parameter metadata key for input `dup_marker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:7:29: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:81:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:82:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:8:13: warning: workflow `test_bam_to_pbam` is missing a parameter metadata key for input `mapq_thresh` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:97:14: warning: task `samtools_flagstat` is missing a parameter metadata key for input `bam` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:98:28: warning: task `samtools_flagstat` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bam_to_pbam.wdl" -message = "/dev/test/test_task/test_bam_to_pbam.wdl:9:17: warning: workflow `test_bam_to_pbam` is missing a parameter metadata key for input `no_dup_removal` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:113:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:114:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:115:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:116:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:13:16: warning: workflow `test_bowtie2` is missing a parameter metadata key for input `ref_pe_flagstat` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:14:16: warning: workflow `test_bowtie2` is missing a parameter metadata key for input `ref_se_flagstat` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:14:31: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:15:16: warning: workflow `test_bowtie2` is missing a parameter metadata key for input `ref_pe_local_flagstat` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:16:16: warning: workflow `test_bowtie2` is missing a parameter metadata key for input `ref_se_local_flagstat` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:18:16: warning: workflow `test_bowtie2` is missing a parameter metadata key for input `pe_bowtie2_idx_tar` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:19:16: warning: workflow `test_bowtie2` is missing a parameter metadata key for input `se_bowtie2_idx_tar` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:20:16: warning: workflow `test_bowtie2` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:34:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:36:25: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:53:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:55:25: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:73:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:75:25: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:7:21: warning: input name `pe_fastqs_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:7:21: warning: workflow `test_bowtie2` is missing a parameter metadata key for input `pe_fastqs_R1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:8:21: warning: input name `pe_fastqs_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:8:21: warning: workflow `test_bowtie2` is missing a parameter metadata key for input `pe_fastqs_R2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:92:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:94:25: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bowtie2.wdl" -message = "/dev/test/test_task/test_bowtie2.wdl:9:21: warning: workflow `test_bowtie2` is missing a parameter metadata key for input `se_fastqs` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl" -message = "/dev/test/test_task/test_bwa.wdl:13:16: warning: workflow `test_bwa` is missing a parameter metadata key for input `ref_pe_flagstat` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl" -message = "/dev/test/test_task/test_bwa.wdl:14:16: warning: workflow `test_bwa` is missing a parameter metadata key for input `ref_se_flagstat` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl" -message = "/dev/test/test_task/test_bwa.wdl:16:16: warning: workflow `test_bwa` is missing a parameter metadata key for input `pe_bwa_idx_tar` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl" -message = "/dev/test/test_task/test_bwa.wdl:17:16: warning: workflow `test_bwa` is missing a parameter metadata key for input `se_bwa_idx_tar` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl" -message = "/dev/test/test_task/test_bwa.wdl:18:16: warning: workflow `test_bwa` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl" -message = "/dev/test/test_task/test_bwa.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl" -message = "/dev/test/test_task/test_bwa.wdl:32:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl" -message = "/dev/test/test_task/test_bwa.wdl:34:25: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl" -message = "/dev/test/test_task/test_bwa.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl" -message = "/dev/test/test_task/test_bwa.wdl:51:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl" -message = "/dev/test/test_task/test_bwa.wdl:53:25: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl" -message = "/dev/test/test_task/test_bwa.wdl:72:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl" -message = "/dev/test/test_task/test_bwa.wdl:73:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl" -message = "/dev/test/test_task/test_bwa.wdl:7:21: warning: input name `pe_fastqs_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl" -message = "/dev/test/test_task/test_bwa.wdl:7:21: warning: workflow `test_bwa` is missing a parameter metadata key for input `pe_fastqs_R1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl" -message = "/dev/test/test_task/test_bwa.wdl:8:21: warning: input name `pe_fastqs_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl" -message = "/dev/test/test_task/test_bwa.wdl:8:21: warning: workflow `test_bwa` is missing a parameter metadata key for input `pe_fastqs_R2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_bwa.wdl" -message = "/dev/test/test_task/test_bwa.wdl:9:21: warning: workflow `test_bwa` is missing a parameter metadata key for input `se_fastqs` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:10:16: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `se_ta_pooled` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:11:16: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `se_ctl_ta_rep1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:12:16: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `se_ctl_ta_rep2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:13:16: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `se_ctl_ta_pooled` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:150:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:151:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:152:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:153:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:154:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:156:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:157:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:158:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:159:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:15:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_idx1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:160:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:162:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:163:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:164:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:166:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:167:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:168:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:169:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:16:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_idx2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:170:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:172:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:173:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:174:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:175:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:176:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:178:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:179:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:17:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_sub1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:180:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:181:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:182:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:184:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:185:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:186:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:187:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:188:10: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:18:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_sub2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:19:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_sub_pooled` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:203:1: warning: more than one blank line in a row [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:206:16: warning: task `raise_exception_and_print` is missing a parameter metadata key for input `msg` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:207:24: warning: task `raise_exception_and_print` is missing a parameter metadata key for input `vals` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:209:28: warning: task `raise_exception_and_print` is missing a parameter metadata key for input `runtime_environment` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:211:5: warning: task `raise_exception_and_print` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:213:32: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:217:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:21:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_always_use_pooled_ctl_idx1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:222:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:224:17: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:22:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_always_use_pooled_ctl_idx2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:23:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_always_use_pooled_ctl_sub1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:24:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_always_use_pooled_ctl_sub2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:25:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_always_use_pooled_ctl_sub_pooled` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:27:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_single_rep_idx1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:28:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_single_rep_sub1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:29:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_single_rep_sub_pooled` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:31:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_single_ctl_idx1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:32:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_single_ctl_idx2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:33:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_single_ctl_sub1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:34:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_single_ctl_sub2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:35:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_single_ctl_sub_pooled` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:37:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_disabled_idx1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:38:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_disabled_idx2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:39:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_disabled_sub1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:40:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_disabled_sub2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:41:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_disabled_sub_pooled` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:43:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_ctl_depth_limit_only_idx1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:44:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_ctl_depth_limit_only_idx2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:45:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_ctl_depth_limit_only_sub1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:46:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_ctl_depth_limit_only_sub2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:47:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_ctl_depth_limit_only_sub_pooled` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:49:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_exp_ctl_depth_ratio_limit_only_idx1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:50:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_exp_ctl_depth_ratio_limit_only_idx2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:51:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_exp_ctl_depth_ratio_limit_only_sub1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:52:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_exp_ctl_depth_ratio_limit_only_sub2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:53:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ref_se_choose_ctl_exp_ctl_depth_ratio_limit_only_sub_pooled` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:55:15: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ctl_depth_ratio` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:56:13: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `ctl_depth_limit` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:57:15: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `exp_ctl_depth_ratio_limit` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:58:16: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:5:27: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:8:16: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `se_ta_rep1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_choose_ctl.wdl" -message = "/dev/test/test_task/test_choose_ctl.wdl:9:16: warning: workflow `test_choose_ctl` is missing a parameter metadata key for input `se_ta_rep2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_count_signal_track.wdl" -message = "/dev/test/test_task/test_count_signal_track.wdl:10:16: warning: workflow `test_count_signal_track` is missing a parameter metadata key for input `ref_se_count_signal_track_neg_bw` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_count_signal_track.wdl" -message = "/dev/test/test_task/test_count_signal_track.wdl:12:16: warning: workflow `test_count_signal_track` is missing a parameter metadata key for input `se_chrsz` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_count_signal_track.wdl" -message = "/dev/test/test_task/test_count_signal_track.wdl:13:16: warning: workflow `test_count_signal_track` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_count_signal_track.wdl" -message = "/dev/test/test_task/test_count_signal_track.wdl:29:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_count_signal_track.wdl" -message = "/dev/test/test_task/test_count_signal_track.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_count_signal_track.wdl" -message = "/dev/test/test_task/test_count_signal_track.wdl:30:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_count_signal_track.wdl" -message = "/dev/test/test_task/test_count_signal_track.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_count_signal_track.wdl" -message = "/dev/test/test_task/test_count_signal_track.wdl:7:16: warning: workflow `test_count_signal_track` is missing a parameter metadata key for input `se_ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_count_signal_track.wdl" -message = "/dev/test/test_task/test_count_signal_track.wdl:9:16: warning: workflow `test_count_signal_track` is missing a parameter metadata key for input `ref_se_count_signal_track_pos_bw` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:100:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:108:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:109:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:10:16: warning: workflow `test_filter` is missing a parameter metadata key for input `pe_bam` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:110:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:111:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:11:16: warning: workflow `test_filter` is missing a parameter metadata key for input `se_bam` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:13:16: warning: workflow `test_filter` is missing a parameter metadata key for input `chrsz` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:15:16: warning: workflow `test_filter` is missing a parameter metadata key for input `ref_pe_nodup_samstat_qc` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:16:16: warning: workflow `test_filter` is missing a parameter metadata key for input `ref_pe_filt_samstat_qc` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:17:16: warning: workflow `test_filter` is missing a parameter metadata key for input `ref_se_nodup_samstat_qc` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:18:16: warning: workflow `test_filter` is missing a parameter metadata key for input `ref_se_filt_samstat_qc` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:19:16: warning: workflow `test_filter` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:26:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:46:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:64:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:7:16: warning: workflow `test_filter` is missing a parameter metadata key for input `dup_marker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:7:29: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:82:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:8:13: warning: workflow `test_filter` is missing a parameter metadata key for input `mapq_thresh` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_filter.wdl" -message = "/dev/test/test_task/test_filter.wdl:9:17: warning: workflow `test_filter` is missing a parameter metadata key for input `no_dup_removal` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_gc_bias.wdl" -message = "/dev/test/test_task/test_gc_bias.wdl:10:16: warning: workflow `test_gc_bias` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_gc_bias.wdl" -message = "/dev/test/test_task/test_gc_bias.wdl:18:32: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_gc_bias.wdl" -message = "/dev/test/test_task/test_gc_bias.wdl:21:28: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_gc_bias.wdl" -message = "/dev/test/test_task/test_gc_bias.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_gc_bias.wdl" -message = "/dev/test/test_task/test_gc_bias.wdl:35:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_gc_bias.wdl" -message = "/dev/test/test_task/test_gc_bias.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_gc_bias.wdl" -message = "/dev/test/test_task/test_gc_bias.wdl:46:6: warning: task `remove_comments_from_gc_log` is missing a runtime section [rule: MissingRuntime]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_gc_bias.wdl" -message = "/dev/test/test_task/test_gc_bias.wdl:48:14: warning: task `remove_comments_from_gc_log` is missing a parameter metadata key for input `gc_log` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_gc_bias.wdl" -message = "/dev/test/test_task/test_gc_bias.wdl:50:5: warning: task `remove_comments_from_gc_log` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_gc_bias.wdl" -message = "/dev/test/test_task/test_gc_bias.wdl:52:36: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_gc_bias.wdl" -message = "/dev/test/test_task/test_gc_bias.wdl:55:33: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_gc_bias.wdl" -message = "/dev/test/test_task/test_gc_bias.wdl:7:14: warning: workflow `test_gc_bias` is missing a parameter metadata key for input `nodup_bam` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_gc_bias.wdl" -message = "/dev/test/test_task/test_gc_bias.wdl:8:14: warning: workflow `test_gc_bias` is missing a parameter metadata key for input `ref_fa` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_gc_bias.wdl" -message = "/dev/test/test_task/test_gc_bias.wdl:9:14: warning: workflow `test_gc_bias` is missing a parameter metadata key for input `ref_gc_log` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:10:16: warning: workflow `test_idr` is missing a parameter metadata key for input `se_peak_rep2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:11:16: warning: workflow `test_idr` is missing a parameter metadata key for input `se_peak_pooled` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:12:16: warning: workflow `test_idr` is missing a parameter metadata key for input `se_ta_pooled` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:14:16: warning: workflow `test_idr` is missing a parameter metadata key for input `ref_se_idr_peak` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:15:16: warning: workflow `test_idr` is missing a parameter metadata key for input `ref_se_idr_bfilt_peak` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:16:16: warning: workflow `test_idr` is missing a parameter metadata key for input `ref_se_idr_frip_qc` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:18:16: warning: workflow `test_idr` is missing a parameter metadata key for input `se_blacklist` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:19:16: warning: workflow `test_idr` is missing a parameter metadata key for input `se_chrsz` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:20:13: warning: workflow `test_idr` is missing a parameter metadata key for input `fraglen` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:21:16: warning: workflow `test_idr` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:29:40: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:31:38: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:32:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:37:21: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:38:16: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:50:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:51:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:52:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:7:15: warning: workflow `test_idr` is missing a parameter metadata key for input `idr_thresh` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_idr.wdl" -message = "/dev/test/test_task/test_idr.wdl:9:16: warning: workflow `test_idr` is missing a parameter metadata key for input `se_peak_rep1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_jsd.wdl" -message = "/dev/test/test_task/test_jsd.wdl:10:21: warning: workflow `test_jsd` is missing a parameter metadata key for input `ref_se_jsd_logs` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_jsd.wdl" -message = "/dev/test/test_task/test_jsd.wdl:11:16: warning: workflow `test_jsd` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_jsd.wdl" -message = "/dev/test/test_task/test_jsd.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_jsd.wdl" -message = "/dev/test/test_task/test_jsd.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_jsd.wdl" -message = "/dev/test/test_task/test_jsd.wdl:52:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_jsd.wdl" -message = "/dev/test/test_task/test_jsd.wdl:53:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_jsd.wdl" -message = "/dev/test/test_task/test_jsd.wdl:70:6: warning: task `take_8_cols` is missing a runtime section [rule: MissingRuntime]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_jsd.wdl" -message = "/dev/test/test_task/test_jsd.wdl:72:14: warning: task `take_8_cols` is missing a parameter metadata key for input `f` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_jsd.wdl" -message = "/dev/test/test_task/test_jsd.wdl:74:5: warning: task `take_8_cols` uses curly braces in command section [rule: NoCurlyCommands]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_jsd.wdl" -message = "/dev/test/test_task/test_jsd.wdl:78:20: warning: string defined 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"/dev/test/test_task/test_macs2.wdl:10:13: warning: workflow `test_macs2` is missing a parameter metadata key for input `fraglen` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:12:16: warning: workflow `test_macs2` is missing a parameter metadata key for input `se_ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:13:16: warning: workflow `test_macs2` is missing a parameter metadata key for input `se_ctl_ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:15:16: warning: workflow `test_macs2` is missing a parameter metadata key for input `ref_se_macs2_npeak` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:16:16: warning: workflow `test_macs2` is missing a parameter metadata key for input `ref_se_macs2_bfilt_npeak` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:17:16: warning: workflow `test_macs2` is missing a parameter metadata key for input `ref_se_macs2_frip_qc` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:17:36: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:19:16: warning: workflow `test_macs2` is missing a parameter metadata key for input `se_blacklist` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:20:16: warning: workflow `test_macs2` is missing a parameter metadata key for input `se_chrsz` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:21:16: warning: workflow `test_macs2` is missing a parameter metadata key for input `se_gensz` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:22:16: warning: workflow `test_macs2` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:30:40: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:37:23: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:38:21: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:51:41: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:57:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:58:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:59:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:7:13: warning: workflow `test_macs2` is missing a parameter metadata key for input `cap_num_peak` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2.wdl" -message = "/dev/test/test_task/test_macs2.wdl:8:15: warning: workflow `test_macs2` is missing a parameter metadata key for input `pval_thresh` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2_signal_track.wdl" -message = "/dev/test/test_task/test_macs2_signal_track.wdl:11:16: warning: workflow `test_macs2_signal_track` is missing a parameter metadata key for input `se_ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2_signal_track.wdl" -message = "/dev/test/test_task/test_macs2_signal_track.wdl:12:16: warning: workflow `test_macs2_signal_track` is missing a parameter metadata key for input `se_ctl_ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2_signal_track.wdl" -message = "/dev/test/test_task/test_macs2_signal_track.wdl:14:16: warning: workflow `test_macs2_signal_track` is missing a parameter metadata key for input `ref_se_macs2_pval_bw` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2_signal_track.wdl" -message = "/dev/test/test_task/test_macs2_signal_track.wdl:15:16: warning: workflow `test_macs2_signal_track` is missing a parameter metadata key for input `se_chrsz` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2_signal_track.wdl" -message = "/dev/test/test_task/test_macs2_signal_track.wdl:16:16: warning: workflow `test_macs2_signal_track` is missing a parameter metadata key for input `se_gensz` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2_signal_track.wdl" -message = "/dev/test/test_task/test_macs2_signal_track.wdl:17:16: warning: workflow `test_macs2_signal_track` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2_signal_track.wdl" -message = "/dev/test/test_task/test_macs2_signal_track.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2_signal_track.wdl" -message = "/dev/test/test_task/test_macs2_signal_track.wdl:38:41: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2_signal_track.wdl" -message = "/dev/test/test_task/test_macs2_signal_track.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2_signal_track.wdl" -message = "/dev/test/test_task/test_macs2_signal_track.wdl:44:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2_signal_track.wdl" -message = "/dev/test/test_task/test_macs2_signal_track.wdl:7:15: warning: workflow `test_macs2_signal_track` is missing a parameter metadata key for input `pval_thresh` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_macs2_signal_track.wdl" -message = "/dev/test/test_task/test_macs2_signal_track.wdl:9:13: warning: workflow `test_macs2_signal_track` is missing a parameter metadata key for input `fraglen` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_overlap.wdl" -message = "/dev/test/test_task/test_overlap.wdl:10:16: warning: workflow `test_overlap` is missing a parameter metadata key for input `se_ta_pooled` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_overlap.wdl" -message = "/dev/test/test_task/test_overlap.wdl:12:16: warning: workflow `test_overlap` is missing a parameter metadata key for input `ref_se_overlap_peak` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_overlap.wdl" -message = "/dev/test/test_task/test_overlap.wdl:13:16: warning: workflow `test_overlap` is missing a parameter metadata key for input `ref_se_overlap_bfilt_peak` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_overlap.wdl" -message = "/dev/test/test_task/test_overlap.wdl:14:16: warning: workflow `test_overlap` is missing a parameter metadata key for input `ref_se_overlap_frip_qc` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_overlap.wdl" -message = "/dev/test/test_task/test_overlap.wdl:16:16: warning: workflow `test_overlap` is missing a parameter metadata key for input `se_blacklist` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_overlap.wdl" -message = "/dev/test/test_task/test_overlap.wdl:17:16: warning: workflow `test_overlap` is missing a parameter metadata key for input `se_chrsz` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_overlap.wdl" -message = "/dev/test/test_task/test_overlap.wdl:18:13: warning: workflow `test_overlap` is missing a parameter metadata key for input `fraglen` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_overlap.wdl" -message = "/dev/test/test_task/test_overlap.wdl:19:16: warning: workflow `test_overlap` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_overlap.wdl" -message = "/dev/test/test_task/test_overlap.wdl:27:40: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_overlap.wdl" -message = "/dev/test/test_task/test_overlap.wdl:29:1: warning: more than one blank line in a row [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_overlap.wdl" -message = "/dev/test/test_task/test_overlap.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_overlap.wdl" -message = "/dev/test/test_task/test_overlap.wdl:31:18: warning: string 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"ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_overlap.wdl" -message = "/dev/test/test_task/test_overlap.wdl:49:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_overlap.wdl" -message = "/dev/test/test_task/test_overlap.wdl:7:16: warning: workflow `test_overlap` is missing a parameter metadata key for input `se_peak_rep1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_overlap.wdl" -message = "/dev/test/test_task/test_overlap.wdl:8:16: warning: workflow `test_overlap` is missing a parameter metadata key for input `se_peak_rep2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_overlap.wdl" -message = "/dev/test/test_task/test_overlap.wdl:9:16: warning: workflow `test_overlap` is missing a parameter metadata key for input `se_peak_pooled` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_pool_ta.wdl" -message = "/dev/test/test_task/test_pool_ta.wdl:10:16: warning: workflow `test_pool_ta` is missing a parameter metadata key for input `ref_se_pooled_ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_pool_ta.wdl" -message = "/dev/test/test_task/test_pool_ta.wdl:11:16: warning: workflow `test_pool_ta` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_pool_ta.wdl" -message = "/dev/test/test_task/test_pool_ta.wdl:26:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_pool_ta.wdl" -message = "/dev/test/test_task/test_pool_ta.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_pool_ta.wdl" -message = "/dev/test/test_task/test_pool_ta.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_pool_ta.wdl" -message = "/dev/test/test_task/test_pool_ta.wdl:7:16: warning: workflow `test_pool_ta` is missing a parameter metadata key for input `se_ta_rep1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_pool_ta.wdl" -message = "/dev/test/test_task/test_pool_ta.wdl:8:16: warning: workflow `test_pool_ta` is missing a parameter metadata key for input `se_ta_rep2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_reproducibility.wdl" -message = "/dev/test/test_task/test_reproducibility.wdl:10:16: warning: workflow `test_reproducibility` is missing a parameter metadata key for input `se_overlap_peak_ppr` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_reproducibility.wdl" -message = "/dev/test/test_task/test_reproducibility.wdl:11:16: warning: workflow `test_reproducibility` is missing a parameter metadata key for input `se_chrsz` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_reproducibility.wdl" -message = "/dev/test/test_task/test_reproducibility.wdl:13:16: warning: workflow `test_reproducibility` is missing a parameter metadata key for input `ref_se_reproducibility_qc` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_reproducibility.wdl" -message = "/dev/test/test_task/test_reproducibility.wdl:14:16: warning: workflow `test_reproducibility` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_reproducibility.wdl" -message = "/dev/test/test_task/test_reproducibility.wdl:23:18: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_reproducibility.wdl" -message = "/dev/test/test_task/test_reproducibility.wdl:27:21: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_reproducibility.wdl" -message = "/dev/test/test_task/test_reproducibility.wdl:27:34: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_reproducibility.wdl" -message = "/dev/test/test_task/test_reproducibility.wdl:28:26: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_reproducibility.wdl" -message = "/dev/test/test_task/test_reproducibility.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_reproducibility.wdl" -message = "/dev/test/test_task/test_reproducibility.wdl:34:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_reproducibility.wdl" -message = "/dev/test/test_task/test_reproducibility.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_reproducibility.wdl" -message = "/dev/test/test_task/test_reproducibility.wdl:7:16: warning: workflow `test_reproducibility` is missing a parameter metadata key for input `se_overlap_peak_rep1_vs_rep2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_reproducibility.wdl" -message = "/dev/test/test_task/test_reproducibility.wdl:8:16: warning: workflow `test_reproducibility` is missing a parameter metadata key for input `se_overlap_peak_rep1_pr` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_reproducibility.wdl" -message = "/dev/test/test_task/test_reproducibility.wdl:9:16: warning: workflow `test_reproducibility` is missing a parameter metadata key for input `se_overlap_peak_rep2_pr` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spp.wdl" -message = "/dev/test/test_task/test_spp.wdl:11:16: warning: workflow `test_spp` is missing a parameter metadata key for input `se_ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spp.wdl" -message = "/dev/test/test_task/test_spp.wdl:12:16: warning: workflow `test_spp` is missing a parameter metadata key for input `se_ctl_ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spp.wdl" -message = "/dev/test/test_task/test_spp.wdl:14:16: warning: workflow `test_spp` is missing a parameter metadata key for input `ref_se_spp_rpeak` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spp.wdl" -message = "/dev/test/test_task/test_spp.wdl:15:16: warning: workflow `test_spp` is missing a parameter metadata key for input `ref_se_spp_bfilt_rpeak` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spp.wdl" -message = "/dev/test/test_task/test_spp.wdl:16:16: warning: workflow `test_spp` is missing a parameter metadata key 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"/dev/test/test_task/test_spp.wdl:28:40: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spp.wdl" -message = "/dev/test/test_task/test_spp.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spp.wdl" -message = "/dev/test/test_task/test_spp.wdl:36:23: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spp.wdl" -message = "/dev/test/test_task/test_spp.wdl:37:21: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spp.wdl" -message = "/dev/test/test_task/test_spp.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spp.wdl" -message = "/dev/test/test_task/test_spp.wdl:56:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spp.wdl" -message = "/dev/test/test_task/test_spp.wdl:57:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spp.wdl" -message = "/dev/test/test_task/test_spp.wdl:58:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spp.wdl" -message = "/dev/test/test_task/test_spp.wdl:7:13: warning: workflow `test_spp` is missing a parameter metadata key for input `cap_num_peak` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spp.wdl" -message = "/dev/test/test_task/test_spp.wdl:9:13: warning: workflow `test_spp` is missing a parameter metadata key for input `fraglen` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spr.wdl" -message = "/dev/test/test_task/test_spr.wdl:10:14: warning: workflow `test_spr` is missing a parameter metadata key for input `ref_pe_ta_pr1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spr.wdl" -message = "/dev/test/test_task/test_spr.wdl:11:14: warning: workflow `test_spr` is missing a parameter metadata key for input `ref_pe_ta_pr2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spr.wdl" -message = "/dev/test/test_task/test_spr.wdl:12:14: warning: workflow `test_spr` is missing a parameter metadata key for input `ref_se_ta_pr1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spr.wdl" -message = "/dev/test/test_task/test_spr.wdl:13:14: warning: workflow `test_spr` is missing a parameter metadata key for input `ref_se_ta_pr2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spr.wdl" -message = "/dev/test/test_task/test_spr.wdl:14:14: warning: workflow `test_spr` is missing a parameter metadata key for input `ref_pe_seed_10_ta_pr1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spr.wdl" -message = "/dev/test/test_task/test_spr.wdl:15:14: warning: workflow `test_spr` is missing a parameter metadata key for input `ref_pe_seed_10_ta_pr2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spr.wdl" -message = "/dev/test/test_task/test_spr.wdl:16:14: warning: workflow `test_spr` is missing a parameter 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"/dev/test/test_task/test_spr.wdl:66:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spr.wdl" -message = "/dev/test/test_task/test_spr.wdl:67:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spr.wdl" -message = "/dev/test/test_task/test_spr.wdl:68:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spr.wdl" -message = "/dev/test/test_task/test_spr.wdl:69:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spr.wdl" -message = "/dev/test/test_task/test_spr.wdl:70:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spr.wdl" -message = "/dev/test/test_task/test_spr.wdl:7:14: warning: workflow `test_spr` is missing a parameter metadata key for input `pe_ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_spr.wdl" -message = "/dev/test/test_task/test_spr.wdl:8:14: warning: workflow `test_spr` is missing a parameter metadata key for input `se_ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_subsample_ctl.wdl" -message = "/dev/test/test_task/test_subsample_ctl.wdl:10:13: warning: workflow `test_subsample_ctl` is missing a parameter metadata key for input `se_subsample` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_subsample_ctl.wdl" -message = "/dev/test/test_task/test_subsample_ctl.wdl:11:14: warning: workflow `test_subsample_ctl` is 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`ref_se_ta_subsampled_trivial` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_subsample_ctl.wdl" -message = "/dev/test/test_task/test_subsample_ctl.wdl:15:16: warning: workflow `test_subsample_ctl` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_subsample_ctl.wdl" -message = "/dev/test/test_task/test_subsample_ctl.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_subsample_ctl.wdl" -message = "/dev/test/test_task/test_subsample_ctl.wdl:33:6: warning: line contains trailing whitespace [rule: Whitespace]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_subsample_ctl.wdl" -message = "/dev/test/test_task/test_subsample_ctl.wdl:3:8: warning: string 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-document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_subsample_ctl.wdl" -message = "/dev/test/test_task/test_subsample_ctl.wdl:69:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_subsample_ctl.wdl" -message = "/dev/test/test_task/test_subsample_ctl.wdl:7:14: warning: workflow `test_subsample_ctl` is missing a parameter metadata key for input `pe_ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_subsample_ctl.wdl" -message = "/dev/test/test_task/test_subsample_ctl.wdl:8:14: warning: workflow `test_subsample_ctl` is missing a parameter metadata key for input `se_ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_subsample_ctl.wdl" -message = "/dev/test/test_task/test_subsample_ctl.wdl:9:13: warning: workflow `test_subsample_ctl` is missing a parameter metadata key for input `pe_subsample` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:108:42: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:119:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:11:13: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `pe_crop_length` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:120:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:121:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:122:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:12:13: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `se_crop_length` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:13:13: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `pe_crop_length_tol` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:14:13: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `se_crop_length_tol` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:17:14: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `ref_pe_cropped_flagstat` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:18:14: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `ref_se_cropped_flagstat` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:19:14: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `ref_pe_cropped_phred33_flagstat` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:20:14: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `ref_se_cropped_phred64_flagstat` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:22:14: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `pe_bowtie2_idx_tar` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:23:14: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `se_bowtie2_idx_tar` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:24:16: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:38:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:40:25: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:57:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:59:25: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:77:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:79:25: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:7:21: warning: input name `pe_fastqs_R1` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:7:21: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `pe_fastqs_R1` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:88:42: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:8:21: warning: input name `pe_fastqs_R2` is not snake_case [rule: SnakeCase]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:8:21: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `pe_fastqs_R2` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:97:19: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:99:25: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_trimmomatic.wdl" -message = "/dev/test/test_task/test_trimmomatic.wdl:9:21: warning: workflow `test_trimmomatic` is missing a parameter metadata key for input `se_fastqs` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" -message = "/dev/test/test_task/test_xcor.wdl:10:16: warning: workflow `test_xcor` is missing a parameter metadata key for input `pe_ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" -message = "/dev/test/test_task/test_xcor.wdl:11:16: warning: workflow `test_xcor` is missing a parameter metadata key for input `se_ta` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" -message = "/dev/test/test_task/test_xcor.wdl:13:16: warning: workflow `test_xcor` is missing a parameter metadata key for input `ref_pe_xcor_log` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" -message = "/dev/test/test_task/test_xcor.wdl:14:16: warning: workflow `test_xcor` is missing a parameter metadata key for input `ref_pe_xcor_log_subsample` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" -message = "/dev/test/test_task/test_xcor.wdl:15:16: warning: workflow `test_xcor` is missing a parameter metadata key for input `ref_se_xcor_log` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" -message = "/dev/test/test_task/test_xcor.wdl:16:16: warning: workflow `test_xcor` is missing a parameter metadata key for input `ref_se_xcor_log_subsample` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" -message = "/dev/test/test_task/test_xcor.wdl:17:16: warning: workflow `test_xcor` is missing a parameter metadata key for input `mito_chr_name` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" -message = "/dev/test/test_task/test_xcor.wdl:17:32: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" -message = "/dev/test/test_task/test_xcor.wdl:18:16: warning: workflow `test_xcor` is missing a parameter metadata key for input `docker` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" -message = "/dev/test/test_task/test_xcor.wdl:2:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" -message = "/dev/test/test_task/test_xcor.wdl:3:8: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" -message = "/dev/test/test_task/test_xcor.wdl:7:13: warning: workflow `test_xcor` is missing a parameter metadata key for input `xcor_subsample` [rule: MatchingParameterMeta]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" -message = "/dev/test/test_task/test_xcor.wdl:81:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" -message = "/dev/test/test_task/test_xcor.wdl:82:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" -message = "/dev/test/test_task/test_xcor.wdl:83:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" -message = "/dev/test/test_task/test_xcor.wdl:84:13: warning: string defined with single quotes [rule: DoubleQuotes]" - -[[diagnostics]] -document = "ENCODE-DCC/chip-seq-pipeline2:/dev/test/test_task/test_xcor.wdl" -message = "/dev/test/test_task/test_xcor.wdl:8:13: warning: workflow `test_xcor` is missing a parameter metadata key for input `xcor_subsample_default` [rule: MatchingParameterMeta]" - [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" message = "/ww-fastq-to-cram.wdl:129:5: note: task `FastqToUnmappedBam` has an extraneous parameter metadata key named `unmapped_bam` [rule: MatchingParameterMeta]" diff --git a/wdl-gauntlet/src/lib.rs b/wdl-gauntlet/src/lib.rs index e89e2afec..9262d2f06 100644 --- a/wdl-gauntlet/src/lib.rs +++ b/wdl-gauntlet/src/lib.rs @@ -190,8 +190,18 @@ pub async fn gauntlet(args: Args) -> Result<()> { Err(diagnostics) => Some(diagnostics), } } - Err(diagnostics) => Some(diagnostics), + Err(diagnostics) => { + // If we're in arena mode, skip over the files that failed to fully parse + // We log those diagnostics as part of the normal gauntlet run. + if args.arena { + trace!("skipping {:?} as it has parse errors", abs_path); + continue; + } + + Some(diagnostics) + } }; + let elapsed = before.elapsed(); total_time += elapsed; From 803bc43bd8eadd862685fadd801d44df3b34e5dc Mon Sep 17 00:00:00 2001 From: Peter Huene Date: Wed, 12 Jun 2024 11:17:43 -0700 Subject: [PATCH 3/6] fix: remove redundant relative paths from diagnostic messages in gauntlet. --- Arena.toml | 106 +++++++++++++-------------- Gauntlet.toml | 158 ++++++++++++++++++++-------------------- wdl-gauntlet/src/lib.rs | 10 ++- 3 files changed, 141 insertions(+), 133 deletions(-) diff --git a/Arena.toml b/Arena.toml index 412287685..1712bab02 100644 --- a/Arena.toml +++ b/Arena.toml @@ -4,213 +4,213 @@ commit_hash = "7dd6c4c7c8c9fc6dcd4eb5ff8f3262cd26d5e7cc" [repositories."stjudecloud/workflows"] identifier = "stjudecloud/workflows" -commit_hash = "a44b18a30fd6192af713fded4bc824f6e77f6ff9" +commit_hash = "84bd23756563f32d144f11aa2e82a76e059a8b61" filters = ["/template/task-templates.wdl"] [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "/ww-fastq-to-cram.wdl:129:5: note: task `FastqToUnmappedBam` has an extraneous parameter metadata key named `unmapped_bam` [rule: MatchingParameterMeta]" +message = "ww-fastq-to-cram.wdl:129:5: note: task `FastqToUnmappedBam` has an extraneous parameter metadata key named `unmapped_bam` [rule: MatchingParameterMeta]" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "/ww-fastq-to-cram.wdl:134:6: warning: task name `ValidateCram` is not snake_case [rule: SnakeCase]" +message = "ww-fastq-to-cram.wdl:134:6: warning: task name `ValidateCram` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "/ww-fastq-to-cram.wdl:165:5: note: task `ValidateCram` has an extraneous parameter metadata key named `validation` [rule: MatchingParameterMeta]" +message = "ww-fastq-to-cram.wdl:165:5: note: task `ValidateCram` has an extraneous parameter metadata key named `validation` [rule: MatchingParameterMeta]" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "/ww-fastq-to-cram.wdl:170:6: warning: task name `MergeBamsToCram` is not snake_case [rule: SnakeCase]" +message = "ww-fastq-to-cram.wdl:170:6: warning: task name `MergeBamsToCram` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "/ww-fastq-to-cram.wdl:202:5: note: task `MergeBamsToCram` has an extraneous parameter metadata key named `cram` [rule: MatchingParameterMeta]" +message = "ww-fastq-to-cram.wdl:202:5: note: task `MergeBamsToCram` has an extraneous parameter metadata key named `cram` [rule: MatchingParameterMeta]" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "/ww-fastq-to-cram.wdl:203:5: note: task `MergeBamsToCram` has an extraneous parameter metadata key named `crai` [rule: MatchingParameterMeta]" +message = "ww-fastq-to-cram.wdl:203:5: note: task `MergeBamsToCram` has an extraneous parameter metadata key named `crai` [rule: MatchingParameterMeta]" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "/ww-fastq-to-cram.wdl:205:1: warning: missing newline at the end of the file [rule: EndingNewline]" +message = "ww-fastq-to-cram.wdl:205:1: warning: missing newline at the end of the file [rule: EndingNewline]" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "/ww-fastq-to-cram.wdl:23:10: warning: workflow name `PairedFastqsToUnmappedCram` is not snake_case [rule: SnakeCase]" +message = "ww-fastq-to-cram.wdl:23:10: warning: workflow name `PairedFastqsToUnmappedCram` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "/ww-fastq-to-cram.wdl:57:13: warning: line contains trailing whitespace [rule: Whitespace]" +message = "ww-fastq-to-cram.wdl:57:13: warning: line contains trailing whitespace [rule: Whitespace]" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "/ww-fastq-to-cram.wdl:74:5: note: workflow `PairedFastqsToUnmappedCram` has an extraneous parameter metadata key named `unmapped_crams` [rule: MatchingParameterMeta]" +message = "ww-fastq-to-cram.wdl:74:5: note: workflow `PairedFastqsToUnmappedCram` has an extraneous parameter metadata key named `unmapped_crams` [rule: MatchingParameterMeta]" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "/ww-fastq-to-cram.wdl:75:5: note: workflow `PairedFastqsToUnmappedCram` has an extraneous parameter metadata key named `unmapped_cram_indexes` [rule: MatchingParameterMeta]" +message = "ww-fastq-to-cram.wdl:75:5: note: workflow `PairedFastqsToUnmappedCram` has an extraneous parameter metadata key named `unmapped_cram_indexes` [rule: MatchingParameterMeta]" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "/ww-fastq-to-cram.wdl:76:5: note: workflow `PairedFastqsToUnmappedCram` has an extraneous parameter metadata key named `validation` [rule: MatchingParameterMeta]" +message = "ww-fastq-to-cram.wdl:76:5: note: workflow `PairedFastqsToUnmappedCram` has an extraneous parameter metadata key named `validation` [rule: MatchingParameterMeta]" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "/ww-fastq-to-cram.wdl:83:6: warning: task name `FastqToUnmappedBam` is not snake_case [rule: SnakeCase]" +message = "ww-fastq-to-cram.wdl:83:6: warning: task name `FastqToUnmappedBam` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "/data_structures/read_group.wdl:32:12: warning: struct member name `ID` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:32:12: warning: struct member name `ID` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "/data_structures/read_group.wdl:33:13: warning: struct member name `BC` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:33:13: warning: struct member name `BC` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "/data_structures/read_group.wdl:34:13: warning: struct member name `CN` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:34:13: warning: struct member name `CN` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "/data_structures/read_group.wdl:35:13: warning: struct member name `DS` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:35:13: warning: struct member name `DS` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "/data_structures/read_group.wdl:36:13: warning: struct member name `DT` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:36:13: warning: struct member name `DT` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "/data_structures/read_group.wdl:37:13: warning: struct member name `FO` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:37:13: warning: struct member name `FO` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "/data_structures/read_group.wdl:38:13: warning: struct member name `KS` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:38:13: warning: struct member name `KS` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "/data_structures/read_group.wdl:39:13: warning: struct member name `LB` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:39:13: warning: struct member name `LB` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "/data_structures/read_group.wdl:40:13: warning: struct member name `PG` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:40:13: warning: struct member name `PG` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "/data_structures/read_group.wdl:41:10: warning: struct member name `PI` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:41:10: warning: struct member name `PI` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "/data_structures/read_group.wdl:42:13: warning: struct member name `PL` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:42:13: warning: struct member name `PL` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "/data_structures/read_group.wdl:43:13: warning: struct member name `PM` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:43:13: warning: struct member name `PM` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "/data_structures/read_group.wdl:44:13: warning: struct member name `PU` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:44:13: warning: struct member name `PU` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "/data_structures/read_group.wdl:45:13: warning: struct member name `SM` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:45:13: warning: struct member name `SM` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" -message = "/tools/gatk4.wdl:107:14: warning: input name `dbSNP_vcf` is not snake_case [rule: SnakeCase]" +message = "gatk4.wdl:107:14: warning: input name `dbSNP_vcf` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" -message = "/tools/gatk4.wdl:108:14: warning: input name `dbSNP_vcf_index` is not snake_case [rule: SnakeCase]" +message = "gatk4.wdl:108:14: warning: input name `dbSNP_vcf_index` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" -message = "/tools/gatk4.wdl:249:14: warning: input name `dbSNP_vcf` is not snake_case [rule: SnakeCase]" +message = "gatk4.wdl:249:14: warning: input name `dbSNP_vcf` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" -message = "/tools/gatk4.wdl:250:14: warning: input name `dbSNP_vcf_index` is not snake_case [rule: SnakeCase]" +message = "gatk4.wdl:250:14: warning: input name `dbSNP_vcf_index` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "/tools/star.wdl:552:13: warning: input name `out_QS_conversion_add` is not snake_case [rule: SnakeCase]" +message = "star.wdl:552:13: warning: input name `out_QS_conversion_add` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "/tools/star.wdl:553:13: warning: input name `out_sam_attr_IH_start` is not snake_case [rule: SnakeCase]" +message = "star.wdl:553:13: warning: input name `out_sam_attr_IH_start` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "/tools/star.wdl:555:13: warning: input name `out_sam_flag_OR` is not snake_case [rule: SnakeCase]" +message = "star.wdl:555:13: warning: input name `out_sam_flag_OR` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "/tools/star.wdl:556:13: warning: input name `out_sam_flag_AND` is not snake_case [rule: SnakeCase]" +message = "star.wdl:556:13: warning: input name `out_sam_flag_AND` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "/tools/star.wdl:564:13: warning: input name `score_gap_GCAG` is not snake_case [rule: SnakeCase]" +message = "star.wdl:564:13: warning: input name `score_gap_GCAG` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "/tools/star.wdl:565:13: warning: input name `score_gap_ATAC` is not snake_case [rule: SnakeCase]" +message = "star.wdl:565:13: warning: input name `score_gap_ATAC` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "/tools/star.wdl:597:13: warning: input name `chim_score_junction_nonGTAG` is not snake_case [rule: SnakeCase]" +message = "star.wdl:597:13: warning: input name `chim_score_junction_nonGTAG` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "/tools/star.wdl:61:13: warning: input name `genome_SA_index_n_bases` is not snake_case [rule: SnakeCase]" +message = "star.wdl:61:13: warning: input name `genome_SA_index_n_bases` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "/tools/star.wdl:62:13: warning: input name `genome_SA_sparse_d` is not snake_case [rule: SnakeCase]" +message = "star.wdl:62:13: warning: input name `genome_SA_sparse_d` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "/tools/star.wdl:818:9: warning: struct member name `GT_AG_and_CT_AC_motif` is not snake_case [rule: SnakeCase]" +message = "star.wdl:818:9: warning: struct member name `GT_AG_and_CT_AC_motif` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "/tools/star.wdl:819:9: warning: struct member name `GC_AG_and_CT_GC_motif` is not snake_case [rule: SnakeCase]" +message = "star.wdl:819:9: warning: struct member name `GC_AG_and_CT_GC_motif` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "/tools/star.wdl:820:9: warning: struct member name `AT_AC_and_GT_AT_motif` is not snake_case [rule: SnakeCase]" +message = "star.wdl:820:9: warning: struct member name `AT_AC_and_GT_AT_motif` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl" -message = "/workflows/reference/gatk-reference.wdl:101:15: warning: output name `dbSNP_vcf` is not snake_case [rule: SnakeCase]" +message = "gatk-reference.wdl:101:15: warning: output name `dbSNP_vcf` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl" -message = "/workflows/reference/gatk-reference.wdl:102:15: warning: output name `dbSNP_vcf_index` is not snake_case [rule: SnakeCase]" +message = "gatk-reference.wdl:102:15: warning: output name `dbSNP_vcf_index` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl" -message = "/workflows/reference/gatk-reference.wdl:40:16: warning: input name `dbSNP_vcf_url` is not snake_case [rule: SnakeCase]" +message = "gatk-reference.wdl:40:16: warning: input name `dbSNP_vcf_url` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl" -message = "/workflows/reference/gatk-reference.wdl:41:16: warning: input name `dbSNP_vcf_name` is not snake_case [rule: SnakeCase]" +message = "gatk-reference.wdl:41:16: warning: input name `dbSNP_vcf_name` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl" -message = "/workflows/reference/gatk-reference.wdl:42:17: warning: input name `dbSNP_vcf_index_url` is not snake_case [rule: SnakeCase]" +message = "gatk-reference.wdl:42:17: warning: input name `dbSNP_vcf_index_url` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl" -message = "/workflows/reference/gatk-reference.wdl:43:17: warning: input name `dbSNP_vcf_index_name` is not snake_case [rule: SnakeCase]" +message = "gatk-reference.wdl:43:17: warning: input name `dbSNP_vcf_index_name` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl" -message = "/workflows/rnaseq/rnaseq-core.wdl:138:13: warning: input name `chim_score_junction_nonGTAG` is not snake_case [rule: SnakeCase]" +message = "rnaseq-core.wdl:138:13: warning: input name `chim_score_junction_nonGTAG` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl" -message = "/workflows/rnaseq/rnaseq-variant-calling.wdl:42:14: warning: input name `dbSNP_vcf` is not snake_case [rule: SnakeCase]" +message = "rnaseq-variant-calling.wdl:42:14: warning: input name `dbSNP_vcf` is not snake_case [rule: SnakeCase]" [[diagnostics]] document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl" -message = "/workflows/rnaseq/rnaseq-variant-calling.wdl:43:14: warning: input name `dbSNP_vcf_index` is not snake_case [rule: SnakeCase]" +message = "rnaseq-variant-calling.wdl:43:14: warning: input name `dbSNP_vcf_index` is not snake_case [rule: SnakeCase]" diff --git a/Gauntlet.toml b/Gauntlet.toml index aebe5ef83..a9224cc45 100644 --- a/Gauntlet.toml +++ b/Gauntlet.toml @@ -8,7 +8,7 @@ commit_hash = "b8057d3e3fa575f45f55f7ac7df47fa9bc5f73e0" [repositories."aws-samples/amazon-omics-tutorials"] identifier = "aws-samples/amazon-omics-tutorials" -commit_hash = "d8e8b48ce8faad50b24779d785cd504baadfb13f" +commit_hash = "6c1ae7111deb8f4af68a3c43bff28c7008873b15" [repositories."biowdl/tasks"] identifier = "biowdl/tasks" @@ -20,7 +20,7 @@ commit_hash = "04057c175d0307f96f3f90e2704a4594ebf4e314" [repositories."broadinstitute/palantir-workflows"] identifier = "broadinstitute/palantir-workflows" -commit_hash = "f211198dd142d5aaadaa69fa6dc4f97a4bb2f8b3" +commit_hash = "1e32078d3b57dcb2291534d0caa30f600d40967e" [repositories."broadinstitute/warp"] identifier = "broadinstitute/warp" @@ -28,7 +28,7 @@ commit_hash = "f094475689311ccf227b39b5f40b70762889566c" [repositories."chanzuckerberg/czid-workflows"] identifier = "chanzuckerberg/czid-workflows" -commit_hash = "0381416a3e855d7a036322464f09c8f087d1c5ba" +commit_hash = "15f611d382212519310a1187ef3fd0e96fe3ef21" [repositories."getwilds/ww-fastq-to-cram"] identifier = "getwilds/ww-fastq-to-cram" @@ -44,7 +44,7 @@ commit_hash = "ee08634f28810e5d6fd1a904fc83f4e67821550e" [repositories."stjudecloud/workflows"] identifier = "stjudecloud/workflows" -commit_hash = "a44b18a30fd6192af713fded4bc824f6e77f6ff9" +commit_hash = "84bd23756563f32d144f11aa2e82a76e059a8b61" filters = ["/template/task-templates.wdl"] [repositories."theiagen/public_health_bioinformatics"] @@ -53,300 +53,300 @@ commit_hash = "092f19a0f610eb0a01757456932519bbbfe2bbd9" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl" -message = "/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl:112:40: error: expected input section, output section, runtime section, metadata section, parameter metadata section, conditional statement, scatter statement, task call statement, or private declaration, but found `{`" +message = "mutec2.wdl:112:40: error: expected input section, output section, runtime section, metadata section, parameter metadata section, conditional statement, scatter statement, task call statement, or private declaration, but found `{`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl" -message = "/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl:112:67: error: expected declaration name, but found `,`" +message = "mutec2.wdl:112:67: error: expected declaration name, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl" -message = "/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl:113:62: error: expected declaration name, but found `,`" +message = "mutec2.wdl:113:62: error: expected declaration name, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl" -message = "/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl:114:71: error: expected declaration name, but found `*`" +message = "mutec2.wdl:114:71: error: expected declaration name, but found `*`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl" -message = "/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl:115:72: error: expected declaration name, but found `*`" +message = "mutec2.wdl:115:72: error: expected declaration name, but found `*`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl" -message = "/example-workflows/gatk-best-practices/workflows/somatic-snps-and-indels/mutec2.wdl:117:5: error: expected import statement, struct definition, task definition, or workflow definition, but found `call` keyword" +message = "mutec2.wdl:117:5: error: expected import statement, struct definition, task definition, or workflow definition, but found `call` keyword" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" -message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:110:29: error: expected runtime key, but found `,`" +message = "alphafold-600.wdl:110:29: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" -message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:111:23: error: expected runtime key, but found `,`" +message = "alphafold-600.wdl:111:23: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" -message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:142:29: error: expected runtime key, but found `,`" +message = "alphafold-600.wdl:142:29: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" -message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:143:23: error: expected runtime key, but found `,`" +message = "alphafold-600.wdl:143:23: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" -message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:174:29: error: expected runtime key, but found `,`" +message = "alphafold-600.wdl:174:29: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" -message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:175:23: error: expected runtime key, but found `,`" +message = "alphafold-600.wdl:175:23: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" -message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:210:29: error: expected runtime key, but found `,`" +message = "alphafold-600.wdl:210:29: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" -message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:211:23: error: expected runtime key, but found `,`" +message = "alphafold-600.wdl:211:23: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" -message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:244:29: error: expected runtime key, but found `,`" +message = "alphafold-600.wdl:244:29: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" -message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:245:23: error: expected runtime key, but found `,`" +message = "alphafold-600.wdl:245:23: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" -message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:284:29: error: expected runtime key, but found `,`" +message = "alphafold-600.wdl:284:29: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" -message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:285:23: error: expected runtime key, but found `,`" +message = "alphafold-600.wdl:285:23: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" -message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:323:29: error: expected runtime key, but found `,`" +message = "alphafold-600.wdl:323:29: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" -message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:324:23: error: expected runtime key, but found `,`" +message = "alphafold-600.wdl:324:23: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" -message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:325:28: error: expected runtime key, but found `,`" +message = "alphafold-600.wdl:325:28: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl" -message = "/example-workflows/protein-folding/workflows/alphafold/alphafold-600.wdl:326:48: error: expected runtime key, but found `,`" +message = "alphafold-600.wdl:326:48: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl" -message = "/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl:58:29: error: expected runtime key, but found `,`" +message = "esmfold.wdl:58:29: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl" -message = "/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl:59:23: error: expected runtime key, but found `,`" +message = "esmfold.wdl:59:23: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl" -message = "/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl:83:29: error: expected runtime key, but found `,`" +message = "esmfold.wdl:83:29: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl" -message = "/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl:84:23: error: expected runtime key, but found `,`" +message = "esmfold.wdl:84:23: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl" -message = "/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl:85:28: error: expected runtime key, but found `,`" +message = "esmfold.wdl:85:28: error: expected runtime key, but found `,`" [[diagnostics]] document = "aws-samples/amazon-omics-tutorials:/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl" -message = "/example-workflows/protein-folding/workflows/esmfold/esmfold.wdl:86:48: error: expected runtime key, but found `,`" +message = "esmfold.wdl:86:48: error: expected runtime key, but found `,`" [[diagnostics]] document = "biowdl/tasks:/bcftools.wdl" -message = '/bcftools.wdl:114:75: error: unknown escape sequence `\_`' +message = 'bcftools.wdl:114:75: error: unknown escape sequence `\_`' [[diagnostics]] document = "biowdl/tasks:/bedtools.wdl" -message = '/bedtools.wdl:27:48: error: unknown escape sequence `\.`' +message = 'bedtools.wdl:27:48: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/bowtie.wdl" -message = '/bowtie.wdl:63:32: error: unknown escape sequence `\.`' +message = 'bowtie.wdl:63:32: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/bowtie.wdl" -message = '/bowtie.wdl:63:39: error: unknown escape sequence `\.`' +message = 'bowtie.wdl:63:39: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/bowtie.wdl" -message = '/bowtie.wdl:63:46: error: unknown escape sequence `\.`' +message = 'bowtie.wdl:63:46: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/bowtie.wdl" -message = '/bowtie.wdl:75:48: error: unknown escape sequence `\.`' +message = 'bowtie.wdl:75:48: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/centrifuge.wdl" -message = '/centrifuge.wdl:122:57: error: unknown escape sequence `\.`' +message = 'centrifuge.wdl:122:57: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/centrifuge.wdl" -message = '/centrifuge.wdl:122:64: error: unknown escape sequence `\.`' +message = 'centrifuge.wdl:122:64: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/centrifuge.wdl" -message = '/centrifuge.wdl:199:57: error: unknown escape sequence `\.`' +message = 'centrifuge.wdl:199:57: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/centrifuge.wdl" -message = '/centrifuge.wdl:199:64: error: unknown escape sequence `\.`' +message = 'centrifuge.wdl:199:64: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/centrifuge.wdl" -message = '/centrifuge.wdl:256:57: error: unknown escape sequence `\.`' +message = 'centrifuge.wdl:256:57: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/centrifuge.wdl" -message = '/centrifuge.wdl:256:64: error: unknown escape sequence `\.`' +message = 'centrifuge.wdl:256:64: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/common.wdl" -message = '/common.wdl:275:45: error: unknown escape sequence `\.`' +message = 'common.wdl:275:45: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/fastqc.wdl" -message = '/fastqc.wdl:59:42: error: unknown escape sequence `\.`' +message = 'fastqc.wdl:59:42: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/fastqc.wdl" -message = '/fastqc.wdl:63:54: error: unknown escape sequence `\.`' +message = 'fastqc.wdl:63:54: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/fastqc.wdl" -message = '/fastqc.wdl:63:58: error: unknown escape sequence `\.`' +message = 'fastqc.wdl:63:58: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/gatk.wdl" -message = '/gatk.wdl:127:57: error: unknown escape sequence `\.`' +message = 'gatk.wdl:127:57: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/gatk.wdl" -message = '/gatk.wdl:1597:41: error: unknown escape sequence `\.`' +message = 'gatk.wdl:1597:41: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/hisat2.wdl" -message = '/hisat2.wdl:60:34: error: unknown escape sequence `\.`' +message = 'hisat2.wdl:60:34: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/hisat2.wdl" -message = '/hisat2.wdl:60:41: error: unknown escape sequence `\.`' +message = 'hisat2.wdl:60:41: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/multiqc.wdl" -message = '/multiqc.wdl:133:45: error: unknown escape sequence `\.`' +message = 'multiqc.wdl:133:45: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/picard.wdl" -message = '/picard.wdl:1021:48: error: unknown escape sequence `\.`' +message = 'picard.wdl:1021:48: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/picard.wdl" -message = '/picard.wdl:1191:48: error: unknown escape sequence `\.`' +message = 'picard.wdl:1191:48: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/picard.wdl" -message = '/picard.wdl:643:51: error: unknown escape sequence `\.`' +message = 'picard.wdl:643:51: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/picard.wdl" -message = '/picard.wdl:785:51: error: unknown escape sequence `\.`' +message = 'picard.wdl:785:51: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/picard.wdl" -message = '/picard.wdl:900:46: error: unknown escape sequence `\.`' +message = 'picard.wdl:900:46: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/picard.wdl" -message = '/picard.wdl:901:46: error: unknown escape sequence `\.`' +message = 'picard.wdl:901:46: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/picard.wdl" -message = '/picard.wdl:902:49: error: unknown escape sequence `\.`' +message = 'picard.wdl:902:49: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/sambamba.wdl" -message = '/sambamba.wdl:145:49: error: unknown escape sequence `\.`' +message = 'sambamba.wdl:145:49: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/sambamba.wdl" -message = '/sambamba.wdl:157:60: error: unknown escape sequence `\.`' +message = 'sambamba.wdl:157:60: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/sambamba.wdl" -message = '/sambamba.wdl:91:44: error: unknown escape sequence `\.`' +message = 'sambamba.wdl:91:44: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/samtools.wdl" -message = '/samtools.wdl:238:53: error: unknown escape sequence `\.`' +message = 'samtools.wdl:238:53: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/samtools.wdl" -message = '/samtools.wdl:326:44: error: unknown escape sequence `\.`' +message = 'samtools.wdl:326:44: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/samtools.wdl" -message = '/samtools.wdl:414:44: error: unknown escape sequence `\.`' +message = 'samtools.wdl:414:44: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/samtools.wdl" -message = '/samtools.wdl:458:49: error: unknown escape sequence `\.`' +message = 'samtools.wdl:458:49: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/samtools.wdl" -message = '/samtools.wdl:470:60: error: unknown escape sequence `\.`' +message = 'samtools.wdl:470:60: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/samtools.wdl" -message = '/samtools.wdl:80:42: error: unknown escape sequence `\.`' +message = 'samtools.wdl:80:42: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/umi-tools.wdl" -message = '/umi-tools.wdl:95:49: error: unknown escape sequence `\.`' +message = 'umi-tools.wdl:95:49: error: unknown escape sequence `\.`' [[diagnostics]] document = "biowdl/tasks:/umi.wdl" -message = '/umi.wdl:39:60: error: unknown escape sequence `\.`' +message = 'umi.wdl:39:60: error: unknown escape sequence `\.`' [[diagnostics]] document = "broadinstitute/palantir-workflows:/HaplotypeMap/BuildHaplotypeMap.wdl" -message = "/HaplotypeMap/BuildHaplotypeMap.wdl:17:1: error: a WDL document must start with a version statement" +message = "BuildHaplotypeMap.wdl:17:1: error: a WDL document must start with a version statement" [[diagnostics]] document = "broadinstitute/warp:/pipelines/skylab/scATAC/scATAC.wdl" -message = "/pipelines/skylab/scATAC/scATAC.wdl:203:9: error: duplicate key `cpu` in runtime section" +message = "scATAC.wdl:203:9: error: duplicate key `cpu` in runtime section" [[diagnostics]] document = "broadinstitute/warp:/tasks/broad/GermlineVariantDiscovery.wdl" -message = "/tasks/broad/GermlineVariantDiscovery.wdl:137:32: error: expected string, but found integer" +message = "GermlineVariantDiscovery.wdl:137:32: error: expected string, but found integer" [[diagnostics]] document = "broadinstitute/warp:/tasks/broad/GermlineVariantDiscovery.wdl" -message = "/tasks/broad/GermlineVariantDiscovery.wdl:65:32: error: expected string, but found integer" +message = "GermlineVariantDiscovery.wdl:65:32: error: expected string, but found integer" [[diagnostics]] document = "broadinstitute/warp:/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl" -message = "/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl:814:27: error: expected string, but found integer" +message = "UltimaGenomicsWholeGenomeGermlineTasks.wdl:814:27: error: expected string, but found integer" [[diagnostics]] document = "broadinstitute/warp:/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl" -message = "/tasks/broad/UltimaGenomicsWholeGenomeGermlineTasks.wdl:866:27: error: expected string, but found integer" +message = "UltimaGenomicsWholeGenomeGermlineTasks.wdl:866:27: error: expected string, but found integer" [[diagnostics]] document = "broadinstitute/warp:/tests/cemba/pr/CheckCembaOutputs.wdl" -message = "/tests/cemba/pr/CheckCembaOutputs.wdl:1:1: error: a WDL document must start with a version statement" +message = "CheckCembaOutputs.wdl:1:1: error: a WDL document must start with a version statement" [[diagnostics]] document = "chanzuckerberg/czid-workflows:/workflows/index-generation/index-generation.wdl" -message = "/workflows/index-generation/index-generation.wdl:1:9: error: unsupported WDL version `development`" +message = "index-generation.wdl:1:9: error: unsupported WDL version `development`" diff --git a/wdl-gauntlet/src/lib.rs b/wdl-gauntlet/src/lib.rs index 9262d2f06..b12152df0 100644 --- a/wdl-gauntlet/src/lib.rs +++ b/wdl-gauntlet/src/lib.rs @@ -6,6 +6,7 @@ #![warn(clippy::missing_docs_in_private_items)] #![warn(rustdoc::broken_intra_doc_links)] +use std::path::Path; use std::path::PathBuf; use std::process; use std::time::Duration; @@ -208,7 +209,14 @@ pub async fn gauntlet(args: Args) -> Result<()> { // Convert the diagnostics to a set of short-form messages let mut actual = IndexSet::new(); if let Some(diagnostics) = diagnostics { - let file: SimpleFile<_, _> = SimpleFile::new(document_identifier.path(), source); + let file: SimpleFile<_, _> = SimpleFile::new( + Path::new(document_identifier.path()) + .file_name() + .expect("should have file name") + .to_str() + .expect("path should be UTF-8"), + source, + ); let config = codespan_reporting::term::Config { display_style: DisplayStyle::Short, ..Default::default() From aef0fade6fb4aef702ad3bb714f6c91eaea91ea6 Mon Sep 17 00:00:00 2001 From: Peter Huene Date: Wed, 12 Jun 2024 13:28:25 -0700 Subject: [PATCH 4/6] fix: use `code` in codespan diagnostic for rule name. This commit removes the suffix `[rule: ]` from lint diagnostics in favor of just using the "code" in the codespan diagnostic, which will instead use: ``` []: message ``` --- Arena.toml | 104 +++++++++--------- wdl-grammar/src/experimental/diagnostic.rs | 6 +- .../command-mixed-line-cont/source.errors | 6 +- .../command-mixed-spaces-first/source.errors | 6 +- .../command-mixed-tabs-first/source.errors | 6 +- .../command-mixed-trailing/source.errors | 2 +- .../lints/command-mixed-ws-ok/source.errors | 2 +- .../tests/lints/command-mixed/source.errors | 6 +- .../tests/lints/curly-command/source.errors | 2 +- .../tests/lints/double-quotes/source.errors | 6 +- .../invalid-preamble-comment/source.errors | 4 +- .../lints/matching-param-meta/source.errors | 8 +- .../lints/missing-comment-space/source.errors | 2 +- .../lints/missing-eof-newline/source.errors | 2 +- .../lints/missing-preamble-ws/source.errors | 2 +- .../lints/missing-runtime-block/source.errors | 2 +- .../lints/multiple-eof-newline/source.errors | 2 +- .../tests/lints/only-whitespace/source.errors | 14 +-- .../source.errors | 6 +- .../tests/lints/preamble-ws/source.errors | 4 +- wdl-lint/tests/lints/snake-case/source.errors | 12 +- .../too-many-pounds-preamble/source.errors | 4 +- .../tests/lints/two-eof-newline/source.errors | 2 +- .../unnecessary-preamble-ws/source.errors | 4 +- .../lints/ws-after-blank-line/source.errors | 2 +- .../lints/ws-before-version/source.errors | 2 +- .../lints/ws-preamble-comments/source.errors | 4 +- 27 files changed, 111 insertions(+), 111 deletions(-) diff --git a/Arena.toml b/Arena.toml index 1712bab02..405e77a88 100644 --- a/Arena.toml +++ b/Arena.toml @@ -9,208 +9,208 @@ filters = ["/template/task-templates.wdl"] [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "ww-fastq-to-cram.wdl:129:5: note: task `FastqToUnmappedBam` has an extraneous parameter metadata key named `unmapped_bam` [rule: MatchingParameterMeta]" +message = "ww-fastq-to-cram.wdl:129:5: note[MatchingParameterMeta]: task `FastqToUnmappedBam` has an extraneous parameter metadata key named `unmapped_bam`" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "ww-fastq-to-cram.wdl:134:6: warning: task name `ValidateCram` is not snake_case [rule: SnakeCase]" +message = "ww-fastq-to-cram.wdl:134:6: warning[SnakeCase]: task name `ValidateCram` is not snake_case" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "ww-fastq-to-cram.wdl:165:5: note: task `ValidateCram` has an extraneous parameter metadata key named `validation` [rule: MatchingParameterMeta]" +message = "ww-fastq-to-cram.wdl:165:5: note[MatchingParameterMeta]: task `ValidateCram` has an extraneous parameter metadata key named `validation`" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "ww-fastq-to-cram.wdl:170:6: warning: task name `MergeBamsToCram` is not snake_case [rule: SnakeCase]" +message = "ww-fastq-to-cram.wdl:170:6: warning[SnakeCase]: task name `MergeBamsToCram` is not snake_case" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "ww-fastq-to-cram.wdl:202:5: note: task `MergeBamsToCram` has an extraneous parameter metadata key named `cram` [rule: MatchingParameterMeta]" +message = "ww-fastq-to-cram.wdl:202:5: note[MatchingParameterMeta]: task `MergeBamsToCram` has an extraneous parameter metadata key named `cram`" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "ww-fastq-to-cram.wdl:203:5: note: task `MergeBamsToCram` has an extraneous parameter metadata key named `crai` [rule: MatchingParameterMeta]" +message = "ww-fastq-to-cram.wdl:203:5: note[MatchingParameterMeta]: task `MergeBamsToCram` has an extraneous parameter metadata key named `crai`" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "ww-fastq-to-cram.wdl:205:1: warning: missing newline at the end of the file [rule: EndingNewline]" +message = "ww-fastq-to-cram.wdl:205:1: warning[EndingNewline]: missing newline at the end of the file" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "ww-fastq-to-cram.wdl:23:10: warning: workflow name `PairedFastqsToUnmappedCram` is not snake_case [rule: SnakeCase]" +message = "ww-fastq-to-cram.wdl:23:10: warning[SnakeCase]: workflow name `PairedFastqsToUnmappedCram` is not snake_case" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "ww-fastq-to-cram.wdl:57:13: warning: line contains trailing whitespace [rule: Whitespace]" +message = "ww-fastq-to-cram.wdl:57:13: warning[Whitespace]: line contains trailing whitespace" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "ww-fastq-to-cram.wdl:74:5: note: workflow `PairedFastqsToUnmappedCram` has an extraneous parameter metadata key named `unmapped_crams` [rule: MatchingParameterMeta]" +message = "ww-fastq-to-cram.wdl:74:5: note[MatchingParameterMeta]: workflow `PairedFastqsToUnmappedCram` has an extraneous parameter metadata key named `unmapped_crams`" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "ww-fastq-to-cram.wdl:75:5: note: workflow `PairedFastqsToUnmappedCram` has an extraneous parameter metadata key named `unmapped_cram_indexes` [rule: MatchingParameterMeta]" +message = "ww-fastq-to-cram.wdl:75:5: note[MatchingParameterMeta]: workflow `PairedFastqsToUnmappedCram` has an extraneous parameter metadata key named `unmapped_cram_indexes`" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "ww-fastq-to-cram.wdl:76:5: note: workflow `PairedFastqsToUnmappedCram` has an extraneous parameter metadata key named `validation` [rule: MatchingParameterMeta]" +message = "ww-fastq-to-cram.wdl:76:5: note[MatchingParameterMeta]: workflow `PairedFastqsToUnmappedCram` has an extraneous parameter metadata key named `validation`" [[diagnostics]] document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" -message = "ww-fastq-to-cram.wdl:83:6: warning: task name `FastqToUnmappedBam` is not snake_case [rule: SnakeCase]" +message = "ww-fastq-to-cram.wdl:83:6: warning[SnakeCase]: task name `FastqToUnmappedBam` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "read_group.wdl:32:12: warning: struct member name `ID` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:32:12: warning[SnakeCase]: struct member name `ID` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "read_group.wdl:33:13: warning: struct member name `BC` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:33:13: warning[SnakeCase]: struct member name `BC` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "read_group.wdl:34:13: warning: struct member name `CN` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:34:13: warning[SnakeCase]: struct member name `CN` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "read_group.wdl:35:13: warning: struct member name `DS` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:35:13: warning[SnakeCase]: struct member name `DS` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "read_group.wdl:36:13: warning: struct member name `DT` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:36:13: warning[SnakeCase]: struct member name `DT` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "read_group.wdl:37:13: warning: struct member name `FO` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:37:13: warning[SnakeCase]: struct member name `FO` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "read_group.wdl:38:13: warning: struct member name `KS` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:38:13: warning[SnakeCase]: struct member name `KS` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "read_group.wdl:39:13: warning: struct member name `LB` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:39:13: warning[SnakeCase]: struct member name `LB` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "read_group.wdl:40:13: warning: struct member name `PG` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:40:13: warning[SnakeCase]: struct member name `PG` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "read_group.wdl:41:10: warning: struct member name `PI` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:41:10: warning[SnakeCase]: struct member name `PI` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "read_group.wdl:42:13: warning: struct member name `PL` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:42:13: warning[SnakeCase]: struct member name `PL` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "read_group.wdl:43:13: warning: struct member name `PM` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:43:13: warning[SnakeCase]: struct member name `PM` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "read_group.wdl:44:13: warning: struct member name `PU` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:44:13: warning[SnakeCase]: struct member name `PU` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" -message = "read_group.wdl:45:13: warning: struct member name `SM` is not snake_case [rule: SnakeCase]" +message = "read_group.wdl:45:13: warning[SnakeCase]: struct member name `SM` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" -message = "gatk4.wdl:107:14: warning: input name `dbSNP_vcf` is not snake_case [rule: SnakeCase]" +message = "gatk4.wdl:107:14: warning[SnakeCase]: input name `dbSNP_vcf` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" -message = "gatk4.wdl:108:14: warning: input name `dbSNP_vcf_index` is not snake_case [rule: SnakeCase]" +message = "gatk4.wdl:108:14: warning[SnakeCase]: input name `dbSNP_vcf_index` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" -message = "gatk4.wdl:249:14: warning: input name `dbSNP_vcf` is not snake_case [rule: SnakeCase]" +message = "gatk4.wdl:249:14: warning[SnakeCase]: input name `dbSNP_vcf` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/tools/gatk4.wdl" -message = "gatk4.wdl:250:14: warning: input name `dbSNP_vcf_index` is not snake_case [rule: SnakeCase]" +message = "gatk4.wdl:250:14: warning[SnakeCase]: input name `dbSNP_vcf_index` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "star.wdl:552:13: warning: input name `out_QS_conversion_add` is not snake_case [rule: SnakeCase]" +message = "star.wdl:552:13: warning[SnakeCase]: input name `out_QS_conversion_add` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "star.wdl:553:13: warning: input name `out_sam_attr_IH_start` is not snake_case [rule: SnakeCase]" +message = "star.wdl:553:13: warning[SnakeCase]: input name `out_sam_attr_IH_start` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "star.wdl:555:13: warning: input name `out_sam_flag_OR` is not snake_case [rule: SnakeCase]" +message = "star.wdl:555:13: warning[SnakeCase]: input name `out_sam_flag_OR` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "star.wdl:556:13: warning: input name `out_sam_flag_AND` is not snake_case [rule: SnakeCase]" +message = "star.wdl:556:13: warning[SnakeCase]: input name `out_sam_flag_AND` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "star.wdl:564:13: warning: input name `score_gap_GCAG` is not snake_case [rule: SnakeCase]" +message = "star.wdl:564:13: warning[SnakeCase]: input name `score_gap_GCAG` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "star.wdl:565:13: warning: input name `score_gap_ATAC` is not snake_case [rule: SnakeCase]" +message = "star.wdl:565:13: warning[SnakeCase]: input name `score_gap_ATAC` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "star.wdl:597:13: warning: input name `chim_score_junction_nonGTAG` is not snake_case [rule: SnakeCase]" +message = "star.wdl:597:13: warning[SnakeCase]: input name `chim_score_junction_nonGTAG` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "star.wdl:61:13: warning: input name `genome_SA_index_n_bases` is not snake_case [rule: SnakeCase]" +message = "star.wdl:61:13: warning[SnakeCase]: input name `genome_SA_index_n_bases` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "star.wdl:62:13: warning: input name `genome_SA_sparse_d` is not snake_case [rule: SnakeCase]" +message = "star.wdl:62:13: warning[SnakeCase]: input name `genome_SA_sparse_d` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "star.wdl:818:9: warning: struct member name `GT_AG_and_CT_AC_motif` is not snake_case [rule: SnakeCase]" +message = "star.wdl:818:9: warning[SnakeCase]: struct member name `GT_AG_and_CT_AC_motif` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "star.wdl:819:9: warning: struct member name `GC_AG_and_CT_GC_motif` is not snake_case [rule: SnakeCase]" +message = "star.wdl:819:9: warning[SnakeCase]: struct member name `GC_AG_and_CT_GC_motif` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/tools/star.wdl" -message = "star.wdl:820:9: warning: struct member name `AT_AC_and_GT_AT_motif` is not snake_case [rule: SnakeCase]" +message = "star.wdl:820:9: warning[SnakeCase]: struct member name `AT_AC_and_GT_AT_motif` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl" -message = "gatk-reference.wdl:101:15: warning: output name `dbSNP_vcf` is not snake_case [rule: SnakeCase]" +message = "gatk-reference.wdl:101:15: warning[SnakeCase]: output name `dbSNP_vcf` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl" -message = "gatk-reference.wdl:102:15: warning: output name `dbSNP_vcf_index` is not snake_case [rule: SnakeCase]" +message = "gatk-reference.wdl:102:15: warning[SnakeCase]: output name `dbSNP_vcf_index` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl" -message = "gatk-reference.wdl:40:16: warning: input name `dbSNP_vcf_url` is not snake_case [rule: SnakeCase]" +message = "gatk-reference.wdl:40:16: warning[SnakeCase]: input name `dbSNP_vcf_url` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl" -message = "gatk-reference.wdl:41:16: warning: input name `dbSNP_vcf_name` is not snake_case [rule: SnakeCase]" +message = "gatk-reference.wdl:41:16: warning[SnakeCase]: input name `dbSNP_vcf_name` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl" -message = "gatk-reference.wdl:42:17: warning: input name `dbSNP_vcf_index_url` is not snake_case [rule: SnakeCase]" +message = "gatk-reference.wdl:42:17: warning[SnakeCase]: input name `dbSNP_vcf_index_url` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/workflows/reference/gatk-reference.wdl" -message = "gatk-reference.wdl:43:17: warning: input name `dbSNP_vcf_index_name` is not snake_case [rule: SnakeCase]" +message = "gatk-reference.wdl:43:17: warning[SnakeCase]: input name `dbSNP_vcf_index_name` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-core.wdl" -message = "rnaseq-core.wdl:138:13: warning: input name `chim_score_junction_nonGTAG` is not snake_case [rule: SnakeCase]" +message = "rnaseq-core.wdl:138:13: warning[SnakeCase]: input name `chim_score_junction_nonGTAG` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl" -message = "rnaseq-variant-calling.wdl:42:14: warning: input name `dbSNP_vcf` is not snake_case [rule: SnakeCase]" +message = "rnaseq-variant-calling.wdl:42:14: warning[SnakeCase]: input name `dbSNP_vcf` is not snake_case" [[diagnostics]] document = "stjudecloud/workflows:/workflows/rnaseq/rnaseq-variant-calling.wdl" -message = "rnaseq-variant-calling.wdl:43:14: warning: input name `dbSNP_vcf_index` is not snake_case [rule: SnakeCase]" +message = "rnaseq-variant-calling.wdl:43:14: warning[SnakeCase]: input name `dbSNP_vcf_index` is not snake_case" diff --git a/wdl-grammar/src/experimental/diagnostic.rs b/wdl-grammar/src/experimental/diagnostic.rs index 97e235fa4..aa4f9509a 100644 --- a/wdl-grammar/src/experimental/diagnostic.rs +++ b/wdl-grammar/src/experimental/diagnostic.rs @@ -186,11 +186,11 @@ impl Diagnostic { }; if let Some(rule) = &self.rule { - diagnostic.message = format!("{msg} [rule: {rule}]", msg = self.message); - } else { - diagnostic.message.clone_from(&self.message); + diagnostic.code = Some(rule.clone()); } + diagnostic.message.clone_from(&self.message); + if let Some(fix) = &self.fix { diagnostic.notes.push(format!("fix: {fix}")); } diff --git a/wdl-lint/tests/lints/command-mixed-line-cont/source.errors b/wdl-lint/tests/lints/command-mixed-line-cont/source.errors index 9584554a7..09fb375ec 100644 --- a/wdl-lint/tests/lints/command-mixed-line-cont/source.errors +++ b/wdl-lint/tests/lints/command-mixed-line-cont/source.errors @@ -1,4 +1,4 @@ -warning: mixed indentation within a command [rule: CommandSectionMixedIndentation] +warning[CommandSectionMixedIndentation]: mixed indentation within a command ┌─ tests/lints/command-mixed-line-cont/source.wdl:8:2 │ 6 │ command <<< @@ -9,7 +9,7 @@ warning: mixed indentation within a command [rule: CommandSectionMixedIndentatio │ = fix: use the same whitespace character for indentation -warning: task `test2` uses curly braces in command section [rule: NoCurlyCommands] +warning[NoCurlyCommands]: task `test2` uses curly braces in command section ┌─ tests/lints/command-mixed-line-cont/source.wdl:15:5 │ 15 │ command { @@ -17,7 +17,7 @@ warning: task `test2` uses curly braces in command section [rule: NoCurlyCommand │ = fix: instead of curly braces, use heredoc syntax (<<<>>>>) for command sections -warning: mixed indentation within a command [rule: CommandSectionMixedIndentation] +warning[CommandSectionMixedIndentation]: mixed indentation within a command ┌─ tests/lints/command-mixed-line-cont/source.wdl:17:2 │ 15 │ command { diff --git a/wdl-lint/tests/lints/command-mixed-spaces-first/source.errors b/wdl-lint/tests/lints/command-mixed-spaces-first/source.errors index 0cf36aed8..b3593cc90 100644 --- a/wdl-lint/tests/lints/command-mixed-spaces-first/source.errors +++ b/wdl-lint/tests/lints/command-mixed-spaces-first/source.errors @@ -1,4 +1,4 @@ -warning: mixed indentation within a command [rule: CommandSectionMixedIndentation] +warning[CommandSectionMixedIndentation]: mixed indentation within a command ┌─ tests/lints/command-mixed-spaces-first/source.wdl:8:1 │ 6 │ command <<< @@ -9,7 +9,7 @@ warning: mixed indentation within a command [rule: CommandSectionMixedIndentatio │ = fix: use the same whitespace character for indentation -warning: task `test2` uses curly braces in command section [rule: NoCurlyCommands] +warning[NoCurlyCommands]: task `test2` uses curly braces in command section ┌─ tests/lints/command-mixed-spaces-first/source.wdl:15:5 │ 15 │ command { @@ -17,7 +17,7 @@ warning: task `test2` uses curly braces in command section [rule: NoCurlyCommand │ = fix: instead of curly braces, use heredoc syntax (<<<>>>>) for command sections -warning: mixed indentation within a command [rule: CommandSectionMixedIndentation] +warning[CommandSectionMixedIndentation]: mixed indentation within a command ┌─ tests/lints/command-mixed-spaces-first/source.wdl:17:1 │ 15 │ command { diff --git a/wdl-lint/tests/lints/command-mixed-tabs-first/source.errors b/wdl-lint/tests/lints/command-mixed-tabs-first/source.errors index ab7d0573b..f113955e2 100644 --- a/wdl-lint/tests/lints/command-mixed-tabs-first/source.errors +++ b/wdl-lint/tests/lints/command-mixed-tabs-first/source.errors @@ -1,4 +1,4 @@ -warning: mixed indentation within a command [rule: CommandSectionMixedIndentation] +warning[CommandSectionMixedIndentation]: mixed indentation within a command ┌─ tests/lints/command-mixed-tabs-first/source.wdl:8:1 │ 6 │ command <<< @@ -9,7 +9,7 @@ warning: mixed indentation within a command [rule: CommandSectionMixedIndentatio │ = fix: use the same whitespace character for indentation -warning: task `test2` uses curly braces in command section [rule: NoCurlyCommands] +warning[NoCurlyCommands]: task `test2` uses curly braces in command section ┌─ tests/lints/command-mixed-tabs-first/source.wdl:15:5 │ 15 │ command { @@ -17,7 +17,7 @@ warning: task `test2` uses curly braces in command section [rule: NoCurlyCommand │ = fix: instead of curly braces, use heredoc syntax (<<<>>>>) for command sections -warning: mixed indentation within a command [rule: CommandSectionMixedIndentation] +warning[CommandSectionMixedIndentation]: mixed indentation within a command ┌─ tests/lints/command-mixed-tabs-first/source.wdl:17:1 │ 15 │ command { diff --git a/wdl-lint/tests/lints/command-mixed-trailing/source.errors b/wdl-lint/tests/lints/command-mixed-trailing/source.errors index 3a8e18d61..f1d770f0c 100644 --- a/wdl-lint/tests/lints/command-mixed-trailing/source.errors +++ b/wdl-lint/tests/lints/command-mixed-trailing/source.errors @@ -1,4 +1,4 @@ -warning: task `test2` uses curly braces in command section [rule: NoCurlyCommands] +warning[NoCurlyCommands]: task `test2` uses curly braces in command section ┌─ tests/lints/command-mixed-trailing/source.wdl:15:5 │ 15 │ command { diff --git a/wdl-lint/tests/lints/command-mixed-ws-ok/source.errors b/wdl-lint/tests/lints/command-mixed-ws-ok/source.errors index 8bea0664c..48787b2fe 100644 --- a/wdl-lint/tests/lints/command-mixed-ws-ok/source.errors +++ b/wdl-lint/tests/lints/command-mixed-ws-ok/source.errors @@ -1,4 +1,4 @@ -warning: task `test2` uses curly braces in command section [rule: NoCurlyCommands] +warning[NoCurlyCommands]: task `test2` uses curly braces in command section ┌─ tests/lints/command-mixed-ws-ok/source.wdl:20:5 │ 20 │ command { diff --git a/wdl-lint/tests/lints/command-mixed/source.errors b/wdl-lint/tests/lints/command-mixed/source.errors index 56c776e2c..825f53071 100644 --- a/wdl-lint/tests/lints/command-mixed/source.errors +++ b/wdl-lint/tests/lints/command-mixed/source.errors @@ -1,4 +1,4 @@ -warning: mixed indentation within a command [rule: CommandSectionMixedIndentation] +warning[CommandSectionMixedIndentation]: mixed indentation within a command ┌─ tests/lints/command-mixed/source.wdl:7:3 │ 6 │ command <<< @@ -8,7 +8,7 @@ warning: mixed indentation within a command [rule: CommandSectionMixedIndentatio │ = fix: use the same whitespace character for indentation -warning: task `test2` uses curly braces in command section [rule: NoCurlyCommands] +warning[NoCurlyCommands]: task `test2` uses curly braces in command section ┌─ tests/lints/command-mixed/source.wdl:14:5 │ 14 │ command { @@ -16,7 +16,7 @@ warning: task `test2` uses curly braces in command section [rule: NoCurlyCommand │ = fix: instead of curly braces, use heredoc syntax (<<<>>>>) for command sections -warning: mixed indentation within a command [rule: CommandSectionMixedIndentation] +warning[CommandSectionMixedIndentation]: mixed indentation within a command ┌─ tests/lints/command-mixed/source.wdl:15:3 │ 14 │ command { diff --git a/wdl-lint/tests/lints/curly-command/source.errors b/wdl-lint/tests/lints/curly-command/source.errors index 038b017ef..3557fef46 100644 --- a/wdl-lint/tests/lints/curly-command/source.errors +++ b/wdl-lint/tests/lints/curly-command/source.errors @@ -1,4 +1,4 @@ -warning: task `bad` uses curly braces in command section [rule: NoCurlyCommands] +warning[NoCurlyCommands]: task `bad` uses curly braces in command section ┌─ tests/lints/curly-command/source.wdl:7:5 │ 7 │ command { diff --git a/wdl-lint/tests/lints/double-quotes/source.errors b/wdl-lint/tests/lints/double-quotes/source.errors index 3fdab2546..92734db37 100644 --- a/wdl-lint/tests/lints/double-quotes/source.errors +++ b/wdl-lint/tests/lints/double-quotes/source.errors @@ -1,4 +1,4 @@ -warning: string defined with single quotes [rule: DoubleQuotes] +warning[DoubleQuotes]: string defined with single quotes ┌─ tests/lints/double-quotes/source.wdl:7:18 │ 7 │ String bad = 'this string is not okay' @@ -6,7 +6,7 @@ warning: string defined with single quotes [rule: DoubleQuotes] │ = fix: change the single quotes to double quotes -warning: string defined with single quotes [rule: DoubleQuotes] +warning[DoubleQuotes]: string defined with single quotes ┌─ tests/lints/double-quotes/source.wdl:9:30 │ 9 │ "this string is ok ~{'but this is not and ~{"while this one is okay ~{'this one is not'}"}'}!" @@ -14,7 +14,7 @@ warning: string defined with single quotes [rule: DoubleQuotes] │ = fix: change the single quotes to double quotes -warning: string defined with single quotes [rule: DoubleQuotes] +warning[DoubleQuotes]: string defined with single quotes ┌─ tests/lints/double-quotes/source.wdl:9:79 │ 9 │ "this string is ok ~{'but this is not and ~{"while this one is okay ~{'this one is not'}"}'}!" diff --git a/wdl-lint/tests/lints/invalid-preamble-comment/source.errors b/wdl-lint/tests/lints/invalid-preamble-comment/source.errors index 8f0f6558f..70b52a4f1 100644 --- a/wdl-lint/tests/lints/invalid-preamble-comment/source.errors +++ b/wdl-lint/tests/lints/invalid-preamble-comment/source.errors @@ -1,4 +1,4 @@ -note: preamble comments must start with `##` [rule: PreambleComments] +note[PreambleComments]: preamble comments must start with `##` ┌─ tests/lints/invalid-preamble-comment/source.wdl:1:1 │ 1 │ # This is an invalid preamble comment. @@ -6,7 +6,7 @@ note: preamble comments must start with `##` [rule: PreambleComments] │ = fix: change the comment to start with `##` followed by a space -note: preamble comments must start with `##` [rule: PreambleComments] +note[PreambleComments]: preamble comments must start with `##` ┌─ tests/lints/invalid-preamble-comment/source.wdl:3:1 │ 3 │ # This one is invalid too! diff --git a/wdl-lint/tests/lints/matching-param-meta/source.errors b/wdl-lint/tests/lints/matching-param-meta/source.errors index 214493d86..daa16d895 100644 --- a/wdl-lint/tests/lints/matching-param-meta/source.errors +++ b/wdl-lint/tests/lints/matching-param-meta/source.errors @@ -1,4 +1,4 @@ -warning: task `t` is missing a parameter metadata key for input `does_not_exist` [rule: MatchingParameterMeta] +warning[MatchingParameterMeta]: task `t` is missing a parameter metadata key for input `does_not_exist` ┌─ tests/lints/matching-param-meta/source.wdl:8:16 │ 8 │ String does_not_exist @@ -6,7 +6,7 @@ warning: task `t` is missing a parameter metadata key for input `does_not_exist` │ = fix: add a `does_not_exist` key to the `parameter_meta` section with a detailed description of the input. -note: task `t` has an extraneous parameter metadata key named `extra` [rule: MatchingParameterMeta] +note[MatchingParameterMeta]: task `t` has an extraneous parameter metadata key named `extra` ┌─ tests/lints/matching-param-meta/source.wdl:20:9 │ 20 │ extra: "this should not be here" @@ -14,7 +14,7 @@ note: task `t` has an extraneous parameter metadata key named `extra` [rule: Mat │ = fix: remove the extraneous parameter metadata entry -warning: workflow `w` is missing a parameter metadata key for input `does_not_exist` [rule: MatchingParameterMeta] +warning[MatchingParameterMeta]: workflow `w` is missing a parameter metadata key for input `does_not_exist` ┌─ tests/lints/matching-param-meta/source.wdl:30:16 │ 30 │ String does_not_exist @@ -22,7 +22,7 @@ warning: workflow `w` is missing a parameter metadata key for input `does_not_ex │ = fix: add a `does_not_exist` key to the `parameter_meta` section with a detailed description of the input. -note: workflow `w` has an extraneous parameter metadata key named `extra` [rule: MatchingParameterMeta] +note[MatchingParameterMeta]: workflow `w` has an extraneous parameter metadata key named `extra` ┌─ tests/lints/matching-param-meta/source.wdl:42:9 │ 42 │ extra: "this should not be here" diff --git a/wdl-lint/tests/lints/missing-comment-space/source.errors b/wdl-lint/tests/lints/missing-comment-space/source.errors index c9172b728..3d1c95867 100644 --- a/wdl-lint/tests/lints/missing-comment-space/source.errors +++ b/wdl-lint/tests/lints/missing-comment-space/source.errors @@ -1,4 +1,4 @@ -note: preamble comments must have a space after `##` [rule: PreambleComments] +note[PreambleComments]: preamble comments must have a space after `##` ┌─ tests/lints/missing-comment-space/source.wdl:1:1 │ 1 │ ##This preamble comment is missing a space. diff --git a/wdl-lint/tests/lints/missing-eof-newline/source.errors b/wdl-lint/tests/lints/missing-eof-newline/source.errors index ce74c79fe..b9980fe1b 100644 --- a/wdl-lint/tests/lints/missing-eof-newline/source.errors +++ b/wdl-lint/tests/lints/missing-eof-newline/source.errors @@ -1,4 +1,4 @@ -warning: missing newline at the end of the file [rule: EndingNewline] +warning[EndingNewline]: missing newline at the end of the file ┌─ tests/lints/missing-eof-newline/source.wdl:7:1 │ 7 │ } diff --git a/wdl-lint/tests/lints/missing-preamble-ws/source.errors b/wdl-lint/tests/lints/missing-preamble-ws/source.errors index b467867bc..3fbddd122 100644 --- a/wdl-lint/tests/lints/missing-preamble-ws/source.errors +++ b/wdl-lint/tests/lints/missing-preamble-ws/source.errors @@ -1,4 +1,4 @@ -note: expected a blank line before the version statement [rule: PreambleWhitespace] +note[PreambleWhitespace]: expected a blank line before the version statement ┌─ tests/lints/missing-preamble-ws/source.wdl:1:50 │ 1 │ ## This is a test of missing preamble whitespace. diff --git a/wdl-lint/tests/lints/missing-runtime-block/source.errors b/wdl-lint/tests/lints/missing-runtime-block/source.errors index 407fd1db7..a30a81b8f 100644 --- a/wdl-lint/tests/lints/missing-runtime-block/source.errors +++ b/wdl-lint/tests/lints/missing-runtime-block/source.errors @@ -1,4 +1,4 @@ -warning: task `bad` is missing a runtime section [rule: MissingRuntime] +warning[MissingRuntime]: task `bad` is missing a runtime section ┌─ tests/lints/missing-runtime-block/source.wdl:5:6 │ 5 │ task bad { diff --git a/wdl-lint/tests/lints/multiple-eof-newline/source.errors b/wdl-lint/tests/lints/multiple-eof-newline/source.errors index 83350b0e5..df43d1aa7 100644 --- a/wdl-lint/tests/lints/multiple-eof-newline/source.errors +++ b/wdl-lint/tests/lints/multiple-eof-newline/source.errors @@ -1,4 +1,4 @@ -warning: multiple empty lines at the end of file [rule: EndingNewline] +warning[EndingNewline]: multiple empty lines at the end of file ┌─ tests/lints/multiple-eof-newline/source.wdl:7:2 │ 7 │ } diff --git a/wdl-lint/tests/lints/only-whitespace/source.errors b/wdl-lint/tests/lints/only-whitespace/source.errors index 3c16b74a9..64e4368aa 100644 --- a/wdl-lint/tests/lints/only-whitespace/source.errors +++ b/wdl-lint/tests/lints/only-whitespace/source.errors @@ -1,4 +1,4 @@ -warning: line contains only whitespace [rule: Whitespace] +warning[Whitespace]: line contains only whitespace ┌─ tests/lints/only-whitespace/source.wdl:6:1 │ 6 │ @@ -6,7 +6,7 @@ warning: line contains only whitespace [rule: Whitespace] │ = fix: remove the whitespace from this line -warning: line contains only whitespace [rule: Whitespace] +warning[Whitespace]: line contains only whitespace ┌─ tests/lints/only-whitespace/source.wdl:9:1 │ 9 │ @@ -14,7 +14,7 @@ warning: line contains only whitespace [rule: Whitespace] │ = fix: remove the whitespace from this line -warning: more than one blank line in a row [rule: Whitespace] +warning[Whitespace]: more than one blank line in a row ┌─ tests/lints/only-whitespace/source.wdl:9:1 │ 9 │ ╭ @@ -25,7 +25,7 @@ warning: more than one blank line in a row [rule: Whitespace] │ = fix: remove the unnecessary blank lines -warning: line contains trailing whitespace [rule: Whitespace] +warning[Whitespace]: line contains trailing whitespace ┌─ tests/lints/only-whitespace/source.wdl:12:16 │ 12 │ workflow test { @@ -33,7 +33,7 @@ warning: line contains trailing whitespace [rule: Whitespace] │ = fix: remove the trailing whitespace from this line -warning: line contains only whitespace [rule: Whitespace] +warning[Whitespace]: line contains only whitespace ┌─ tests/lints/only-whitespace/source.wdl:13:1 │ 13 │ @@ -41,7 +41,7 @@ warning: line contains only whitespace [rule: Whitespace] │ = fix: remove the whitespace from this line -warning: line contains trailing whitespace [rule: Whitespace] +warning[Whitespace]: line contains trailing whitespace ┌─ tests/lints/only-whitespace/source.wdl:14:18 │ 14 │ String x = "" @@ -49,7 +49,7 @@ warning: line contains trailing whitespace [rule: Whitespace] │ = fix: remove the trailing whitespace from this line -warning: line contains only whitespace [rule: Whitespace] +warning[Whitespace]: line contains only whitespace ┌─ tests/lints/only-whitespace/source.wdl:16:1 │ 16 │ diff --git a/wdl-lint/tests/lints/preamble-comment-after-version/source.errors b/wdl-lint/tests/lints/preamble-comment-after-version/source.errors index cfed7cac8..87b4851e4 100644 --- a/wdl-lint/tests/lints/preamble-comment-after-version/source.errors +++ b/wdl-lint/tests/lints/preamble-comment-after-version/source.errors @@ -1,4 +1,4 @@ -note: unnecessary whitespace in document preamble [rule: PreambleWhitespace] +note[PreambleWhitespace]: unnecessary whitespace in document preamble ┌─ tests/lints/preamble-comment-after-version/source.wdl:2:1 │ 2 │ ## Bad leading whitespace! @@ -6,7 +6,7 @@ note: unnecessary whitespace in document preamble [rule: PreambleWhitespace] │ = fix: remove the unnecessary whitespace -note: preamble comments cannot come after the version statement [rule: PreambleComments] +note[PreambleComments]: preamble comments cannot come after the version statement ┌─ tests/lints/preamble-comment-after-version/source.wdl:6:1 │ 6 │ ## This is a preamble comment after the version @@ -14,7 +14,7 @@ note: preamble comments cannot come after the version statement [rule: PreambleC │ = fix: change the comment to start with `#` followed by a space -note: preamble comments cannot come after the version statement [rule: PreambleComments] +note[PreambleComments]: preamble comments cannot come after the version statement ┌─ tests/lints/preamble-comment-after-version/source.wdl:15:5 │ 15 │ ## This one is bad! diff --git a/wdl-lint/tests/lints/preamble-ws/source.errors b/wdl-lint/tests/lints/preamble-ws/source.errors index 8b37fa510..f9e083d48 100644 --- a/wdl-lint/tests/lints/preamble-ws/source.errors +++ b/wdl-lint/tests/lints/preamble-ws/source.errors @@ -1,4 +1,4 @@ -note: unnecessary whitespace in document preamble [rule: PreambleWhitespace] +note[PreambleWhitespace]: unnecessary whitespace in document preamble ┌─ tests/lints/preamble-ws/source.wdl:2:1 │ 2 │ version 1.1 @@ -6,7 +6,7 @@ note: unnecessary whitespace in document preamble [rule: PreambleWhitespace] │ = fix: remove the unnecessary whitespace -note: expected a blank line before the version statement [rule: PreambleWhitespace] +note[PreambleWhitespace]: expected a blank line before the version statement ┌─ tests/lints/preamble-ws/source.wdl:2:1 │ 2 │ version 1.1 diff --git a/wdl-lint/tests/lints/snake-case/source.errors b/wdl-lint/tests/lints/snake-case/source.errors index 32265a710..a94cc4060 100644 --- a/wdl-lint/tests/lints/snake-case/source.errors +++ b/wdl-lint/tests/lints/snake-case/source.errors @@ -1,4 +1,4 @@ -warning: workflow name `BadWorkflow` is not snake_case [rule: SnakeCase] +warning[SnakeCase]: workflow name `BadWorkflow` is not snake_case ┌─ tests/lints/snake-case/source.wdl:5:10 │ 5 │ workflow BadWorkflow { @@ -6,7 +6,7 @@ warning: workflow name `BadWorkflow` is not snake_case [rule: SnakeCase] │ = fix: replace `BadWorkflow` with `bad_workflow` -warning: private declaration name `badPrivateDecl` is not snake_case [rule: SnakeCase] +warning[SnakeCase]: private declaration name `badPrivateDecl` is not snake_case ┌─ tests/lints/snake-case/source.wdl:6:11 │ 6 │ Float badPrivateDecl = 3.14 @@ -14,7 +14,7 @@ warning: private declaration name `badPrivateDecl` is not snake_case [rule: Snak │ = fix: replace `badPrivateDecl` with `bad_private_decl` -warning: task name `BadTask` is not snake_case [rule: SnakeCase] +warning[SnakeCase]: task name `BadTask` is not snake_case ┌─ tests/lints/snake-case/source.wdl:11:6 │ 11 │ task BadTask { @@ -22,7 +22,7 @@ warning: task name `BadTask` is not snake_case [rule: SnakeCase] │ = fix: replace `BadTask` with `bad_task` -warning: input name `BadInput` is not snake_case [rule: SnakeCase] +warning[SnakeCase]: input name `BadInput` is not snake_case ┌─ tests/lints/snake-case/source.wdl:13:16 │ 13 │ String BadInput @@ -30,7 +30,7 @@ warning: input name `BadInput` is not snake_case [rule: SnakeCase] │ = fix: replace `BadInput` with `bad_input` -warning: output name `badOut` is not snake_case [rule: SnakeCase] +warning[SnakeCase]: output name `badOut` is not snake_case ┌─ tests/lints/snake-case/source.wdl:26:14 │ 26 │ File badOut = "out.txt" @@ -38,7 +38,7 @@ warning: output name `badOut` is not snake_case [rule: SnakeCase] │ = fix: replace `badOut` with `bad_out` -warning: struct member name `bAdFiElD` is not snake_case [rule: SnakeCase] +warning[SnakeCase]: struct member name `bAdFiElD` is not snake_case ┌─ tests/lints/snake-case/source.wdl:54:12 │ 54 │ String bAdFiElD # unfortunately, `convert-case` doesn't understand sarcasm case diff --git a/wdl-lint/tests/lints/too-many-pounds-preamble/source.errors b/wdl-lint/tests/lints/too-many-pounds-preamble/source.errors index f11263500..bff5fa513 100644 --- a/wdl-lint/tests/lints/too-many-pounds-preamble/source.errors +++ b/wdl-lint/tests/lints/too-many-pounds-preamble/source.errors @@ -1,4 +1,4 @@ -note: preamble comments cannot start with more than two `#` [rule: PreambleComments] +note[PreambleComments]: preamble comments cannot start with more than two `#` ┌─ tests/lints/too-many-pounds-preamble/source.wdl:1:1 │ 1 │ ### This comment has too many pound signs! @@ -6,7 +6,7 @@ note: preamble comments cannot start with more than two `#` [rule: PreambleComme │ = fix: change the comment to start with `##` followed by a space -note: preamble comments cannot start with more than two `#` [rule: PreambleComments] +note[PreambleComments]: preamble comments cannot start with more than two `#` ┌─ tests/lints/too-many-pounds-preamble/source.wdl:3:1 │ 3 │ ###### This comment also has too many pound signs! diff --git a/wdl-lint/tests/lints/two-eof-newline/source.errors b/wdl-lint/tests/lints/two-eof-newline/source.errors index e10c84e13..fccedce9d 100644 --- a/wdl-lint/tests/lints/two-eof-newline/source.errors +++ b/wdl-lint/tests/lints/two-eof-newline/source.errors @@ -1,4 +1,4 @@ -warning: multiple empty lines at the end of file [rule: EndingNewline] +warning[EndingNewline]: multiple empty lines at the end of file ┌─ tests/lints/two-eof-newline/source.wdl:7:2 │ 7 │ } diff --git a/wdl-lint/tests/lints/unnecessary-preamble-ws/source.errors b/wdl-lint/tests/lints/unnecessary-preamble-ws/source.errors index 47616b6b0..9408b8df0 100644 --- a/wdl-lint/tests/lints/unnecessary-preamble-ws/source.errors +++ b/wdl-lint/tests/lints/unnecessary-preamble-ws/source.errors @@ -1,4 +1,4 @@ -note: unnecessary whitespace in document preamble [rule: PreambleWhitespace] +note[PreambleWhitespace]: unnecessary whitespace in document preamble ┌─ tests/lints/unnecessary-preamble-ws/source.wdl:4:1 │ 4 │ @@ -6,7 +6,7 @@ note: unnecessary whitespace in document preamble [rule: PreambleWhitespace] │ = fix: remove the unnecessary whitespace -note: unnecessary whitespace in document preamble [rule: PreambleWhitespace] +note[PreambleWhitespace]: unnecessary whitespace in document preamble ┌─ tests/lints/unnecessary-preamble-ws/source.wdl:5:1 │ 5 │ ╭ diff --git a/wdl-lint/tests/lints/ws-after-blank-line/source.errors b/wdl-lint/tests/lints/ws-after-blank-line/source.errors index cf98924bb..f28b2c9c5 100644 --- a/wdl-lint/tests/lints/ws-after-blank-line/source.errors +++ b/wdl-lint/tests/lints/ws-after-blank-line/source.errors @@ -1,4 +1,4 @@ -note: unnecessary whitespace in document preamble [rule: PreambleWhitespace] +note[PreambleWhitespace]: unnecessary whitespace in document preamble ┌─ tests/lints/ws-after-blank-line/source.wdl:3:1 │ 3 │ ╭ diff --git a/wdl-lint/tests/lints/ws-before-version/source.errors b/wdl-lint/tests/lints/ws-before-version/source.errors index 3aff4f14a..142b7918a 100644 --- a/wdl-lint/tests/lints/ws-before-version/source.errors +++ b/wdl-lint/tests/lints/ws-before-version/source.errors @@ -1,4 +1,4 @@ -note: unnecessary whitespace in document preamble [rule: PreambleWhitespace] +note[PreambleWhitespace]: unnecessary whitespace in document preamble ┌─ tests/lints/ws-before-version/source.wdl:1:1 │ 1 │ ╭ diff --git a/wdl-lint/tests/lints/ws-preamble-comments/source.errors b/wdl-lint/tests/lints/ws-preamble-comments/source.errors index 08dc45da1..a945b2e59 100644 --- a/wdl-lint/tests/lints/ws-preamble-comments/source.errors +++ b/wdl-lint/tests/lints/ws-preamble-comments/source.errors @@ -1,4 +1,4 @@ -note: unnecessary whitespace in document preamble [rule: PreambleWhitespace] +note[PreambleWhitespace]: unnecessary whitespace in document preamble ┌─ tests/lints/ws-preamble-comments/source.wdl:2:1 │ 2 │ ╭ @@ -8,7 +8,7 @@ note: unnecessary whitespace in document preamble [rule: PreambleWhitespace] │ = fix: remove the unnecessary whitespace -note: unnecessary whitespace in document preamble [rule: PreambleWhitespace] +note[PreambleWhitespace]: unnecessary whitespace in document preamble ┌─ tests/lints/ws-preamble-comments/source.wdl:5:1 │ 5 │ ╭ From 54223027db3e5bea2fa2e5a09c0f28c198ae0968 Mon Sep 17 00:00:00 2001 From: Peter Huene Date: Wed, 12 Jun 2024 15:46:15 -0700 Subject: [PATCH 5/6] fix: emit only one diagnostic for consecutive comment tokens. This fixes the `PreambleComments` rule to emit a single diagnostic for any number of consecutive (excluding whitespace) comments. --- wdl-lint/src/v1/preamble_comments.rs | 90 ++++++++++--------- .../invalid-preamble-comment/source.errors | 8 +- .../lints/missing-comment-space/source.errors | 4 +- .../source.errors | 32 +++++++ .../one-invalid-preamble-comment/source.wdl | 18 ++++ .../source.errors | 4 +- .../too-many-pounds-preamble/source.errors | 8 +- 7 files changed, 112 insertions(+), 52 deletions(-) create mode 100644 wdl-lint/tests/lints/one-invalid-preamble-comment/source.errors create mode 100644 wdl-lint/tests/lints/one-invalid-preamble-comment/source.wdl diff --git a/wdl-lint/src/v1/preamble_comments.rs b/wdl-lint/src/v1/preamble_comments.rs index 9097d5284..8170bd87e 100644 --- a/wdl-lint/src/v1/preamble_comments.rs +++ b/wdl-lint/src/v1/preamble_comments.rs @@ -6,6 +6,7 @@ use wdl_ast::experimental::Comment; use wdl_ast::experimental::Diagnostic; use wdl_ast::experimental::Diagnostics; use wdl_ast::experimental::Span; +use wdl_ast::experimental::SyntaxKind; use wdl_ast::experimental::VersionStatement; use wdl_ast::experimental::VisitReason; @@ -18,26 +19,10 @@ const ID: &str = "PreambleComments"; /// Creates an "invalid preamble comment" diagnostic. fn invalid_preamble_comment(span: Span) -> Diagnostic { - Diagnostic::note("preamble comments must start with `##`") + Diagnostic::note("preamble comments must start with `##` followed by a space") .with_rule(ID) .with_highlight(span) - .with_fix("change the comment to start with `##` followed by a space") -} - -/// Creates a "too many pound signs" diagnostic. -fn too_many_pound_signs(span: Span) -> Diagnostic { - Diagnostic::note("preamble comments cannot start with more than two `#`") - .with_rule(ID) - .with_highlight(span) - .with_fix("change the comment to start with `##` followed by a space") -} - -/// Creates a "missing space" diagnostic. -fn missing_space(span: Span) -> Diagnostic { - Diagnostic::note("preamble comments must have a space after `##`") - .with_rule(ID) - .with_highlight(span) - .with_fix("add a space between `##` and the start of the comment") + .with_fix("change each preamble comment to start with `##` followed by a space") } /// Creates a "preamble comment after version" diagnostic. @@ -45,7 +30,7 @@ fn preamble_comment_after_version(span: Span) -> Diagnostic { Diagnostic::note("preamble comments cannot come after the version statement") .with_rule(ID) .with_highlight(span) - .with_fix("change the comment to start with `#` followed by a space") + .with_fix("change each comment to start with `#` followed by a space") } /// Detects incorrect comments in a document preamble. @@ -89,6 +74,8 @@ impl Rule for PreambleCommentsRule { struct PreambleCommentsVisitor { /// Whether or not the preamble has finished. finished: bool, + /// The number of comment tokens to skip. + skip_count: usize, } impl Visitor for PreambleCommentsVisitor { @@ -109,34 +96,57 @@ impl Visitor for PreambleCommentsVisitor { } fn comment(&mut self, state: &mut Self::State, comment: &Comment) { - let text = comment.as_str(); - if self.finished { - if let Some(text) = text.strip_prefix("##") { - if !text.starts_with('#') { - state.add(preamble_comment_after_version(comment.span())); - } - } - + // Skip this comment if necessary; this occurs if we've consolidated multiple + // comments in a row into a single diagnostic + if self.skip_count > 0 { + self.skip_count -= 1; return; } - if let Some(text) = text.strip_prefix("##") { - // Check for too many pound signs - if text.starts_with('#') { - state.add(too_many_pound_signs(comment.span())); - return; - } + let check = |text: &str| { + let double_pound = text == "##" || text.starts_with("## "); + (self.finished && !double_pound) || (!self.finished && double_pound) + }; + + if check(comment.as_str()) { + // The comment is valid, stop here + return; + } - // Check for missing space - if !text.is_empty() && !text.starts_with(' ') { - state.add(missing_space(comment.span())); - return; + // Otherwise, look for the next siblings that might also be invalid; + // if so, consolidate them into a single diagnostic + let mut span = comment.span(); + let mut current = comment.syntax().next_sibling_or_token(); + while let Some(sibling) = current { + match sibling.kind() { + SyntaxKind::Comment => { + // As we're processing this sibling comment here, increment the skip count + self.skip_count += 1; + + if check(sibling.as_token().expect("should be a token").text()) { + // The comment is valid, stop here + break; + } + + // Not valid, update the span + span = Span::new( + span.start(), + usize::from(sibling.text_range().end()) - span.start(), + ); + } + SyntaxKind::Whitespace => { + // Skip whitespace + } + _ => break, } - // Valid preamble comment - return; + current = sibling.next_sibling_or_token(); } - state.add(invalid_preamble_comment(comment.span())); + if self.finished { + state.add(preamble_comment_after_version(span)); + } else { + state.add(invalid_preamble_comment(span)); + } } } diff --git a/wdl-lint/tests/lints/invalid-preamble-comment/source.errors b/wdl-lint/tests/lints/invalid-preamble-comment/source.errors index 70b52a4f1..0d7cbb6ee 100644 --- a/wdl-lint/tests/lints/invalid-preamble-comment/source.errors +++ b/wdl-lint/tests/lints/invalid-preamble-comment/source.errors @@ -1,16 +1,16 @@ -note[PreambleComments]: preamble comments must start with `##` +note[PreambleComments]: preamble comments must start with `##` followed by a space ┌─ tests/lints/invalid-preamble-comment/source.wdl:1:1 │ 1 │ # This is an invalid preamble comment. │ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ │ - = fix: change the comment to start with `##` followed by a space + = fix: change each preamble comment to start with `##` followed by a space -note[PreambleComments]: preamble comments must start with `##` +note[PreambleComments]: preamble comments must start with `##` followed by a space ┌─ tests/lints/invalid-preamble-comment/source.wdl:3:1 │ 3 │ # This one is invalid too! │ ^^^^^^^^^^^^^^^^^^^^^^^^^^ │ - = fix: change the comment to start with `##` followed by a space + = fix: change each preamble comment to start with `##` followed by a space diff --git a/wdl-lint/tests/lints/missing-comment-space/source.errors b/wdl-lint/tests/lints/missing-comment-space/source.errors index 3d1c95867..c6adcacea 100644 --- a/wdl-lint/tests/lints/missing-comment-space/source.errors +++ b/wdl-lint/tests/lints/missing-comment-space/source.errors @@ -1,8 +1,8 @@ -note[PreambleComments]: preamble comments must have a space after `##` +note[PreambleComments]: preamble comments must start with `##` followed by a space ┌─ tests/lints/missing-comment-space/source.wdl:1:1 │ 1 │ ##This preamble comment is missing a space. │ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ │ - = fix: add a space between `##` and the start of the comment + = fix: change each preamble comment to start with `##` followed by a space diff --git a/wdl-lint/tests/lints/one-invalid-preamble-comment/source.errors b/wdl-lint/tests/lints/one-invalid-preamble-comment/source.errors new file mode 100644 index 000000000..20d590eff --- /dev/null +++ b/wdl-lint/tests/lints/one-invalid-preamble-comment/source.errors @@ -0,0 +1,32 @@ +note[PreambleComments]: preamble comments must start with `##` followed by a space + ┌─ tests/lints/one-invalid-preamble-comment/source.wdl:1:1 + │ + 1 │ ╭ # This is a test of having one big invalid preamble comment. + 2 │ │ # + 3 │ │ + 4 │ │ # All of the lines + · │ +10 │ │ # as a single diagnostic +11 │ │ # warning + │ ╰─────────^ + │ + = fix: change each preamble comment to start with `##` followed by a space + +note[PreambleWhitespace]: unnecessary whitespace in document preamble + ┌─ tests/lints/one-invalid-preamble-comment/source.wdl:3:1 + │ +3 │ ╭ +4 │ │ # All of the lines + │ ╰^ + │ + = fix: remove the unnecessary whitespace + +note[PreambleWhitespace]: unnecessary whitespace in document preamble + ┌─ tests/lints/one-invalid-preamble-comment/source.wdl:9:1 + │ + 9 │ ╭ +10 │ │ # as a single diagnostic + │ ╰^ + │ + = fix: remove the unnecessary whitespace + diff --git a/wdl-lint/tests/lints/one-invalid-preamble-comment/source.wdl b/wdl-lint/tests/lints/one-invalid-preamble-comment/source.wdl new file mode 100644 index 000000000..43a250cd3 --- /dev/null +++ b/wdl-lint/tests/lints/one-invalid-preamble-comment/source.wdl @@ -0,0 +1,18 @@ +# This is a test of having one big invalid preamble comment. +# + +# All of the lines +# in this comment +# should be treated +# +# + +# as a single diagnostic +# warning +## This last one is fine though! + +version 1.1 + +workflow test { + +} diff --git a/wdl-lint/tests/lints/preamble-comment-after-version/source.errors b/wdl-lint/tests/lints/preamble-comment-after-version/source.errors index 87b4851e4..c774fc251 100644 --- a/wdl-lint/tests/lints/preamble-comment-after-version/source.errors +++ b/wdl-lint/tests/lints/preamble-comment-after-version/source.errors @@ -12,7 +12,7 @@ note[PreambleComments]: preamble comments cannot come after the version statemen 6 │ ## This is a preamble comment after the version │ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ │ - = fix: change the comment to start with `#` followed by a space + = fix: change each comment to start with `#` followed by a space note[PreambleComments]: preamble comments cannot come after the version statement ┌─ tests/lints/preamble-comment-after-version/source.wdl:15:5 @@ -20,5 +20,5 @@ note[PreambleComments]: preamble comments cannot come after the version statemen 15 │ ## This one is bad! │ ^^^^^^^^^^^^^^^^^^^ │ - = fix: change the comment to start with `#` followed by a space + = fix: change each comment to start with `#` followed by a space diff --git a/wdl-lint/tests/lints/too-many-pounds-preamble/source.errors b/wdl-lint/tests/lints/too-many-pounds-preamble/source.errors index bff5fa513..bcfca97c9 100644 --- a/wdl-lint/tests/lints/too-many-pounds-preamble/source.errors +++ b/wdl-lint/tests/lints/too-many-pounds-preamble/source.errors @@ -1,16 +1,16 @@ -note[PreambleComments]: preamble comments cannot start with more than two `#` +note[PreambleComments]: preamble comments must start with `##` followed by a space ┌─ tests/lints/too-many-pounds-preamble/source.wdl:1:1 │ 1 │ ### This comment has too many pound signs! │ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ │ - = fix: change the comment to start with `##` followed by a space + = fix: change each preamble comment to start with `##` followed by a space -note[PreambleComments]: preamble comments cannot start with more than two `#` +note[PreambleComments]: preamble comments must start with `##` followed by a space ┌─ tests/lints/too-many-pounds-preamble/source.wdl:3:1 │ 3 │ ###### This comment also has too many pound signs! │ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ │ - = fix: change the comment to start with `##` followed by a space + = fix: change each preamble comment to start with `##` followed by a space From 51cc206c7aa7c62c1426dda12beb3afff87965f5 Mon Sep 17 00:00:00 2001 From: Peter Huene Date: Wed, 12 Jun 2024 15:48:55 -0700 Subject: [PATCH 6/6] chore: add `getwilds/ww-vc-trio` and `getwilds/ww-star-deseq2` to the arena. --- Arena.toml | 888 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 888 insertions(+) diff --git a/Arena.toml b/Arena.toml index 405e77a88..abbfd43c9 100644 --- a/Arena.toml +++ b/Arena.toml @@ -2,6 +2,14 @@ identifier = "getwilds/ww-fastq-to-cram" commit_hash = "7dd6c4c7c8c9fc6dcd4eb5ff8f3262cd26d5e7cc" +[repositories."getwilds/ww-star-deseq2"] +identifier = "getwilds/ww-star-deseq2" +commit_hash = "3de83fa91db1b2d1b0d91dfc20e3ca71303c8d15" + +[repositories."getwilds/ww-vc-trio"] +identifier = "getwilds/ww-vc-trio" +commit_hash = "ee08634f28810e5d6fd1a904fc83f4e67821550e" + [repositories."stjudecloud/workflows"] identifier = "stjudecloud/workflows" commit_hash = "84bd23756563f32d144f11aa2e82a76e059a8b61" @@ -59,6 +67,886 @@ message = "ww-fastq-to-cram.wdl:76:5: note[MatchingParameterMeta]: workflow `Pai document = "getwilds/ww-fastq-to-cram:/ww-fastq-to-cram.wdl" message = "ww-fastq-to-cram.wdl:83:6: warning[SnakeCase]: task name `FastqToUnmappedBam` is not snake_case" +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:10:22: warning[Whitespace]: line contains trailing whitespace" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:119:5: note[MatchingParameterMeta]: task `FindFastqs` has an extraneous parameter metadata key named `r1_locs`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:120:5: note[MatchingParameterMeta]: task `FindFastqs` has an extraneous parameter metadata key named `r2_locs`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:125:6: warning[SnakeCase]: task name `ConcatenateFastQs` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:133:15: warning[DoubleQuotes]: string defined with single quotes" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:134:15: warning[DoubleQuotes]: string defined with single quotes" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:153:5: note[MatchingParameterMeta]: task `ConcatenateFastQs` has an extraneous parameter metadata key named `r1fastq`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:154:5: note[MatchingParameterMeta]: task `ConcatenateFastQs` has an extraneous parameter metadata key named `r2fastq`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:159:6: warning[SnakeCase]: task name `STARalignTwoPass` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:192:10: warning[SnakeCase]: output name `geneCounts` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:196:10: warning[SnakeCase]: output name `SJout` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:212:5: note[MatchingParameterMeta]: task `STARalignTwoPass` has an extraneous parameter metadata key named `bam`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:213:5: note[MatchingParameterMeta]: task `STARalignTwoPass` has an extraneous parameter metadata key named `bai`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:214:5: note[MatchingParameterMeta]: task `STARalignTwoPass` has an extraneous parameter metadata key named `geneCounts`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:215:5: note[MatchingParameterMeta]: task `STARalignTwoPass` has an extraneous parameter metadata key named `log_final`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:216:5: note[MatchingParameterMeta]: task `STARalignTwoPass` has an extraneous parameter metadata key named `log_progress`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:217:5: note[MatchingParameterMeta]: task `STARalignTwoPass` has an extraneous parameter metadata key named `log`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:218:5: note[MatchingParameterMeta]: task `STARalignTwoPass` has an extraneous parameter metadata key named `SJout`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:225:6: warning[SnakeCase]: task name `RNASeQC` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:255:5: note[MatchingParameterMeta]: task `RNASeQC` has an extraneous parameter metadata key named `rnaseqc_metrics`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:25:36: warning[Whitespace]: line contains trailing whitespace" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:30:13: warning[Whitespace]: line contains trailing whitespace" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:31:43: warning[Whitespace]: line contains trailing whitespace" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:32:43: warning[Whitespace]: line contains trailing whitespace" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:59:17: warning[SnakeCase]: output name `output_geneCounts` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:63:17: warning[SnakeCase]: output name `output_SJ` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:6:10: warning[SnakeCase]: workflow name `STAR2Pass` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:73:5: note[MatchingParameterMeta]: workflow `STAR2Pass` has an extraneous parameter metadata key named `output_bam`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:74:5: note[MatchingParameterMeta]: workflow `STAR2Pass` has an extraneous parameter metadata key named `output_bai`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:75:5: note[MatchingParameterMeta]: workflow `STAR2Pass` has an extraneous parameter metadata key named `output_gene_counts`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:76:5: note[MatchingParameterMeta]: workflow `STAR2Pass` has an extraneous parameter metadata key named `output_log_final`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:77:5: note[MatchingParameterMeta]: workflow `STAR2Pass` has an extraneous parameter metadata key named `output_log_progress`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:78:5: note[MatchingParameterMeta]: workflow `STAR2Pass` has an extraneous parameter metadata key named `output_log`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:79:5: note[MatchingParameterMeta]: workflow `STAR2Pass` has an extraneous parameter metadata key named `output_SJ`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:80:5: note[MatchingParameterMeta]: workflow `STAR2Pass` has an extraneous parameter metadata key named `output_rnaseqc`" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:87:6: warning[SnakeCase]: task name `FindFastqs` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-star-deseq2:/ww-star-deseq2.wdl" +message = "ww-star-deseq2.wdl:9:25: warning[Whitespace]: line contains trailing whitespace" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:136:13: warning[Whitespace]: line contains trailing whitespace" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:145:13: warning[Whitespace]: line contains trailing whitespace" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:19:10: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `batchFile`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:19:10: warning[SnakeCase]: input name `batchFile` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:20:10: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `bedLocation`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:20:10: warning[SnakeCase]: input name `bedLocation` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:217:1: warning[Whitespace]: line contains only whitespace" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:21:12: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `ref_name`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:22:10: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `ref_fasta`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:23:10: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `ref_fasta_index`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:240:76: warning[Whitespace]: line contains trailing whitespace" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:242:17: warning[SnakeCase]: output name `GATK_vcf` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:243:17: warning[SnakeCase]: output name `SAM_vcf` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:244:17: warning[SnakeCase]: output name `Mutect_Vcf` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:245:17: warning[SnakeCase]: output name `Mutect_VcfIndex` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:246:17: warning[SnakeCase]: output name `Mutect_AnnotatedVcf` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:247:17: warning[SnakeCase]: output name `Mutect_AnnotatedTable` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:248:17: warning[SnakeCase]: output name `GATK_annotated_vcf` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:249:17: warning[SnakeCase]: output name `GATK_annotated` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:24:10: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `ref_dict`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:250:17: warning[SnakeCase]: output name `SAM_annotated_vcf` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:251:17: warning[SnakeCase]: output name `SAM_annotated` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:252:17: warning[SnakeCase]: output name `panelQC` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:253:17: warning[SnakeCase]: output name `PicardQC` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:254:17: warning[SnakeCase]: output name `PicardQCpertarget` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:255:17: warning[SnakeCase]: output name `consensusVariants` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:264:10: warning[MatchingParameterMeta]: task `annovar` is missing a parameter metadata key for input `input_vcf`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:265:12: warning[MatchingParameterMeta]: task `annovar` is missing a parameter metadata key for input `ref_name`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:266:12: warning[MatchingParameterMeta]: task `annovar` is missing a parameter metadata key for input `annovar_protocols`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:267:12: warning[MatchingParameterMeta]: task `annovar` is missing a parameter metadata key for input `annovar_operation`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:268:12: warning[MatchingParameterMeta]: task `annovar` is missing a parameter metadata key for input `docker`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:28:11: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `ref_alt`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:298:6: warning[SnakeCase]: task name `ApplyBaseRecalibrator` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:29:10: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `ref_amb`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:2:1: note[PreambleComments]: preamble comments cannot come after the version statement" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:300:10: warning[MatchingParameterMeta]: task `ApplyBaseRecalibrator` is missing a parameter metadata key for input `input_bam`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:301:10: warning[MatchingParameterMeta]: task `ApplyBaseRecalibrator` is missing a parameter metadata key for input `intervals`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:301:19: warning[Whitespace]: line contains trailing whitespace" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:302:10: warning[MatchingParameterMeta]: task `ApplyBaseRecalibrator` is missing a parameter metadata key for input `input_bam_index`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:303:12: warning[MatchingParameterMeta]: task `ApplyBaseRecalibrator` is missing a parameter metadata key for input `base_file_name`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:304:10: warning[MatchingParameterMeta]: task `ApplyBaseRecalibrator` is missing a parameter metadata key for input `dbSNP_vcf`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:304:10: warning[SnakeCase]: input name `dbSNP_vcf` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:305:10: warning[MatchingParameterMeta]: task `ApplyBaseRecalibrator` is missing a parameter metadata key for input `dbSNP_vcf_index`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:305:10: warning[SnakeCase]: input name `dbSNP_vcf_index` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:306:17: warning[MatchingParameterMeta]: task `ApplyBaseRecalibrator` is missing a parameter metadata key for input `known_indels_sites_VCFs`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:306:17: warning[SnakeCase]: input name `known_indels_sites_VCFs` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:307:17: warning[MatchingParameterMeta]: task `ApplyBaseRecalibrator` is missing a parameter metadata key for input `known_indels_sites_indices`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:308:10: warning[MatchingParameterMeta]: task `ApplyBaseRecalibrator` is missing a parameter metadata key for input `ref_dict`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:309:10: warning[MatchingParameterMeta]: task `ApplyBaseRecalibrator` is missing a parameter metadata key for input `ref_fasta`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:30:10: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `ref_ann`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:310:10: warning[MatchingParameterMeta]: task `ApplyBaseRecalibrator` is missing a parameter metadata key for input `ref_fasta_index`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:311:12: warning[MatchingParameterMeta]: task `ApplyBaseRecalibrator` is missing a parameter metadata key for input `docker`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:31:10: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `ref_bwt`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:32:10: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `ref_pac`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:33:10: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `ref_sa`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:342:10: warning[SnakeCase]: output name `sortOrder` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:34:10: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `dbSNP_vcf`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:34:10: warning[SnakeCase]: input name `dbSNP_vcf` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:353:6: warning[SnakeCase]: task name `bcftoolsMpileup` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:355:10: warning[MatchingParameterMeta]: task `bcftoolsMpileup` is missing a parameter metadata key for input `input_bam`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:356:10: warning[MatchingParameterMeta]: task `bcftoolsMpileup` is missing a parameter metadata key for input `input_bam_index`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:357:12: warning[MatchingParameterMeta]: task `bcftoolsMpileup` is missing a parameter metadata key for input `base_file_name`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:358:10: warning[MatchingParameterMeta]: task `bcftoolsMpileup` is missing a parameter metadata key for input `sorted_bed`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:359:10: warning[MatchingParameterMeta]: task `bcftoolsMpileup` is missing a parameter metadata key for input `ref_dict`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:35:10: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `dbSNP_vcf_index`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:35:10: warning[SnakeCase]: input name `dbSNP_vcf_index` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:360:10: warning[MatchingParameterMeta]: task `bcftoolsMpileup` is missing a parameter metadata key for input `ref_fasta`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:361:10: warning[MatchingParameterMeta]: task `bcftoolsMpileup` is missing a parameter metadata key for input `ref_fasta_index`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:362:10: warning[MatchingParameterMeta]: task `bcftoolsMpileup` is missing a parameter metadata key for input `dbSNP_vcf`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:362:10: warning[SnakeCase]: input name `dbSNP_vcf` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:363:12: warning[MatchingParameterMeta]: task `bcftoolsMpileup` is missing a parameter metadata key for input `docker`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:36:17: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `known_indels_sites_VCFs`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:36:17: warning[SnakeCase]: input name `known_indels_sites_VCFs` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:37:17: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `known_indels_sites_indices`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:38:10: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `af_only_gnomad`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:392:6: warning[SnakeCase]: task name `bedToolsQC` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:394:10: warning[MatchingParameterMeta]: task `bedToolsQC` is missing a parameter metadata key for input `input_bam`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:395:10: warning[MatchingParameterMeta]: task `bedToolsQC` is missing a parameter metadata key for input `bed_file`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:396:10: warning[MatchingParameterMeta]: task `bedToolsQC` is missing a parameter metadata key for input `genome_sort_order`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:397:12: warning[MatchingParameterMeta]: task `bedToolsQC` is missing a parameter metadata key for input `base_file_name`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:398:12: warning[MatchingParameterMeta]: task `bedToolsQC` is missing a parameter metadata key for input `docker`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:39:10: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `af_only_gnomad_index`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:409:10: warning[SnakeCase]: output name `meanQC` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:41:12: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `annovar_protocols`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:420:6: warning[SnakeCase]: task name `BwaMem` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:422:10: warning[MatchingParameterMeta]: task `BwaMem` is missing a parameter metadata key for input `input_fastq`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:423:12: warning[MatchingParameterMeta]: task `BwaMem` is missing a parameter metadata key for input `base_file_name`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:424:10: warning[MatchingParameterMeta]: task `BwaMem` is missing a parameter metadata key for input `ref_fasta`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:425:10: warning[MatchingParameterMeta]: task `BwaMem` is missing a parameter metadata key for input `ref_fasta_index`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:426:10: warning[MatchingParameterMeta]: task `BwaMem` is missing a parameter metadata key for input `ref_dict`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:427:11: warning[MatchingParameterMeta]: task `BwaMem` is missing a parameter metadata key for input `ref_alt`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:428:10: warning[MatchingParameterMeta]: task `BwaMem` is missing a parameter metadata key for input `ref_amb`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:429:10: warning[MatchingParameterMeta]: task `BwaMem` is missing a parameter metadata key for input `ref_ann`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:42:12: warning[MatchingParameterMeta]: workflow `ww_vc_trio` is missing a parameter metadata key for input `annovar_operation`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:430:10: warning[MatchingParameterMeta]: task `BwaMem` is missing a parameter metadata key for input `ref_bwt`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:431:10: warning[MatchingParameterMeta]: task `BwaMem` is missing a parameter metadata key for input `ref_pac`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:432:10: warning[MatchingParameterMeta]: task `BwaMem` is missing a parameter metadata key for input `ref_sa`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:433:9: warning[MatchingParameterMeta]: task `BwaMem` is missing a parameter metadata key for input `threads`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:434:12: warning[MatchingParameterMeta]: task `BwaMem` is missing a parameter metadata key for input `docker`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:456:6: warning[SnakeCase]: task name `CollectHsMetrics` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:458:10: warning[MatchingParameterMeta]: task `CollectHsMetrics` is missing a parameter metadata key for input `input_bam`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:459:12: warning[MatchingParameterMeta]: task `CollectHsMetrics` is missing a parameter metadata key for input `base_file_name`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:45:17: warning[SnakeCase]: private declaration name `batchInfo` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:460:10: warning[MatchingParameterMeta]: task `CollectHsMetrics` is missing a parameter metadata key for input `ref_fasta`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:461:10: warning[MatchingParameterMeta]: task `CollectHsMetrics` is missing a parameter metadata key for input `ref_fasta_index`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:462:10: warning[MatchingParameterMeta]: task `CollectHsMetrics` is missing a parameter metadata key for input `intervals`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:463:12: warning[MatchingParameterMeta]: task `CollectHsMetrics` is missing a parameter metadata key for input `docker`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:47:10: warning[SnakeCase]: private declaration name `GATKDocker` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:481:10: warning[SnakeCase]: output name `picardMetrics` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:482:10: warning[SnakeCase]: output name `picardPerTarget` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:48:10: warning[SnakeCase]: private declaration name `bwaDocker` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:492:6: warning[SnakeCase]: task name `consensusProcessingR` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:494:10: warning[MatchingParameterMeta]: task `consensusProcessingR` is missing a parameter metadata key for input `GATKVars`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:494:10: warning[SnakeCase]: input name `GATKVars` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:495:10: warning[MatchingParameterMeta]: task `consensusProcessingR` is missing a parameter metadata key for input `SAMVars`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:495:10: warning[SnakeCase]: input name `SAMVars` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:496:10: warning[MatchingParameterMeta]: task `consensusProcessingR` is missing a parameter metadata key for input `MutectVars`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:496:10: warning[SnakeCase]: input name `MutectVars` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:497:12: warning[MatchingParameterMeta]: task `consensusProcessingR` is missing a parameter metadata key for input `base_file_name`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:498:12: warning[MatchingParameterMeta]: task `consensusProcessingR` is missing a parameter metadata key for input `docker`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:49:10: warning[SnakeCase]: private declaration name `bedtoolsDocker` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:49:61: warning[Whitespace]: line contains trailing whitespace" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:507:10: warning[SnakeCase]: output name `consensusTSV` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:50:10: warning[SnakeCase]: private declaration name `bcftoolsDocker` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:518:6: warning[SnakeCase]: task name `HaplotypeCaller` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:51:10: warning[SnakeCase]: private declaration name `annovarDocker` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:520:10: warning[MatchingParameterMeta]: task `HaplotypeCaller` is missing a parameter metadata key for input `input_bam`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:521:10: warning[MatchingParameterMeta]: task `HaplotypeCaller` is missing a parameter metadata key for input `input_bam_index`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:522:12: warning[MatchingParameterMeta]: task `HaplotypeCaller` is missing a parameter metadata key for input `base_file_name`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:523:10: warning[MatchingParameterMeta]: task `HaplotypeCaller` is missing a parameter metadata key for input `intervals`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:524:10: warning[MatchingParameterMeta]: task `HaplotypeCaller` is missing a parameter metadata key for input `ref_dict`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:525:10: warning[MatchingParameterMeta]: task `HaplotypeCaller` is missing a parameter metadata key for input `ref_fasta`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:526:10: warning[MatchingParameterMeta]: task `HaplotypeCaller` is missing a parameter metadata key for input `ref_fasta_index`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:527:10: warning[MatchingParameterMeta]: task `HaplotypeCaller` is missing a parameter metadata key for input `dbSNP_vcf`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:527:10: warning[SnakeCase]: input name `dbSNP_vcf` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:528:10: warning[MatchingParameterMeta]: task `HaplotypeCaller` is missing a parameter metadata key for input `dbSNP_index`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:528:10: warning[SnakeCase]: input name `dbSNP_index` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:529:12: warning[MatchingParameterMeta]: task `HaplotypeCaller` is missing a parameter metadata key for input `docker`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:52:10: warning[SnakeCase]: private declaration name `RDocker` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:54:7: warning[SnakeCase]: private declaration name `bwaThreads` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:558:6: warning[SnakeCase]: task name `MergeBamAlignment` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:560:10: warning[MatchingParameterMeta]: task `MergeBamAlignment` is missing a parameter metadata key for input `unmapped_bam`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:561:10: warning[MatchingParameterMeta]: task `MergeBamAlignment` is missing a parameter metadata key for input `aligned_bam`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:562:12: warning[MatchingParameterMeta]: task `MergeBamAlignment` is missing a parameter metadata key for input `base_file_name`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:563:10: warning[MatchingParameterMeta]: task `MergeBamAlignment` is missing a parameter metadata key for input `ref_fasta`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:564:10: warning[MatchingParameterMeta]: task `MergeBamAlignment` is missing a parameter metadata key for input `ref_fasta_index`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:565:10: warning[MatchingParameterMeta]: task `MergeBamAlignment` is missing a parameter metadata key for input `ref_dict`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:566:12: warning[MatchingParameterMeta]: task `MergeBamAlignment` is missing a parameter metadata key for input `docker`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:596:6: warning[SnakeCase]: task name `Mutect2TumorOnly` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:598:10: warning[MatchingParameterMeta]: task `Mutect2TumorOnly` is missing a parameter metadata key for input `input_bam`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:599:10: warning[MatchingParameterMeta]: task `Mutect2TumorOnly` is missing a parameter metadata key for input `input_bam_index`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:600:12: warning[MatchingParameterMeta]: task `Mutect2TumorOnly` is missing a parameter metadata key for input `base_file_name`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:601:10: warning[MatchingParameterMeta]: task `Mutect2TumorOnly` is missing a parameter metadata key for input `intervals`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:602:10: warning[MatchingParameterMeta]: task `Mutect2TumorOnly` is missing a parameter metadata key for input `ref_dict`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:603:10: warning[MatchingParameterMeta]: task `Mutect2TumorOnly` is missing a parameter metadata key for input `ref_fasta`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:604:10: warning[MatchingParameterMeta]: task `Mutect2TumorOnly` is missing a parameter metadata key for input `ref_fasta_index`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:605:10: warning[MatchingParameterMeta]: task `Mutect2TumorOnly` is missing a parameter metadata key for input `genomeReference`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:605:10: warning[SnakeCase]: input name `genomeReference` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:606:10: warning[MatchingParameterMeta]: task `Mutect2TumorOnly` is missing a parameter metadata key for input `genomeReferenceIndex`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:606:10: warning[SnakeCase]: input name `genomeReferenceIndex` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:607:12: warning[MatchingParameterMeta]: task `Mutect2TumorOnly` is missing a parameter metadata key for input `docker`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:643:6: warning[SnakeCase]: task name `SamToFastq` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:645:10: warning[MatchingParameterMeta]: task `SamToFastq` is missing a parameter metadata key for input `input_bam`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:646:12: warning[MatchingParameterMeta]: task `SamToFastq` is missing a parameter metadata key for input `base_file_name`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:647:12: warning[MatchingParameterMeta]: task `SamToFastq` is missing a parameter metadata key for input `docker`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:64:12: warning[SnakeCase]: private declaration name `sampleName` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:65:12: warning[SnakeCase]: private declaration name `molecularID` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:66:10: warning[SnakeCase]: private declaration name `sampleBam` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:680:6: warning[SnakeCase]: task name `SortBed` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:682:10: warning[MatchingParameterMeta]: task `SortBed` is missing a parameter metadata key for input `unsorted_bed`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:683:10: warning[MatchingParameterMeta]: task `SortBed` is missing a parameter metadata key for input `ref_dict`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:684:12: warning[MatchingParameterMeta]: task `SortBed` is missing a parameter metadata key for input `docker`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:709:6: warning[SnakeCase]: task name `MarkDuplicates` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:711:10: warning[MatchingParameterMeta]: task `MarkDuplicates` is missing a parameter metadata key for input `input_bam`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:712:12: warning[MatchingParameterMeta]: task `MarkDuplicates` is missing a parameter metadata key for input `output_bam_basename`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:713:12: warning[MatchingParameterMeta]: task `MarkDuplicates` is missing a parameter metadata key for input `metrics_filename`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:714:12: warning[MatchingParameterMeta]: task `MarkDuplicates` is missing a parameter metadata key for input `docker`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:745:6: warning[SnakeCase]: task name `SortSam` is not snake_case" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:747:10: warning[MatchingParameterMeta]: task `SortSam` is missing a parameter metadata key for input `input_bam`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:748:12: warning[MatchingParameterMeta]: task `SortSam` is missing a parameter metadata key for input `base_file_name`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:749:12: warning[MatchingParameterMeta]: task `SortSam` is missing a parameter metadata key for input `docker`" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:771:2: warning[EndingNewline]: multiple empty lines at the end of file" + +[[diagnostics]] +document = "getwilds/ww-vc-trio:/ww-vc-trio.wdl" +message = "ww-vc-trio.wdl:96:1: warning[Whitespace]: line contains only whitespace" + [[diagnostics]] document = "stjudecloud/workflows:/data_structures/read_group.wdl" message = "read_group.wdl:32:12: warning[SnakeCase]: struct member name `ID` is not snake_case"