-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #67 from icgc-argo/validate-seqtools@0.1.6
[release]
- Loading branch information
Showing
8 changed files
with
51 additions
and
24 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
1 change: 1 addition & 0 deletions
1
...sts/expected/anon_chr1_rnaseq.validation_report.PASS-with-WARNING-and-SKIPPED-check.jsonl
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1 @@ | ||
{"tool": {"name": "seq-tools", "version": "1.2.4"}, "metadata_file": "/Users/esu/Desktop/GitHub/icgc-argo/argo-data-submission/validate-seqtools/tests/work/7c/89eab7957d2922c8b8379b03dba2db/local_copy", "data_dir": "/Users/esu/Desktop/GitHub/icgc-argo/argo-data-submission/validate-seqtools/tests/work/7c/89eab7957d2922c8b8379b03dba2db", "started_at": "2023-02-09T20:43:17.966Z", "ended_at": "2023-02-09T20:43:18.170Z", "validation": {"status": "PASS-with-WARNING-and-SKIPPED-check", "message": "Please see individual checks for details", "checks": [{"checker": "c110_rg_id_uniqueness", "status": "PASS", "message": "Read group ID uniqueness check status: PASS"}, {"checker": "c120_permissible_char_in_rg_id", "status": "PASS", "message": "Read group ID permissible character check status: PASS"}, {"checker": "c130_one_sample", "status": "PASS", "message": "One and only one sample check status: PASS"}, {"checker": "c140_platform_unit_uniqueness", "status": "PASS", "message": "Platform unit uniqueness check status: PASS"}, {"checker": "c150_rg_count_match", "status": "PASS", "message": "Read groups count check status: PASS"}, {"checker": "c160_file_r1_r2_check", "status": "PASS", "message": "Fields file_r1 and file_r2 check status: PASS"}, {"checker": "c170_fq_uniqueness_in_rgs", "status": "PASS", "message": "FASTQ uniqueness in read groups check status: PASS"}, {"checker": "c180_file_uniqueness", "status": "PASS", "message": "Files uniqueness check in files section status: PASS"}, {"checker": "c190_no_extra_files", "status": "PASS", "message": "No extra files check status: PASS"}, {"checker": "c200_rg_id_in_bam_uniqueness", "status": "PASS", "message": "'read_group_id_in_bam' uniqueness check status: PASS"}, {"checker": "c210_no_path_in_filename", "status": "PASS", "message": "No path in fileName check in 'files' section status: PASS"}, {"checker": "c220_no_rg_id_in_bam_for_fq", "status": "PASS", "message": "'read_group_id_in_bam' not populated for FASTQ check: PASS"}, {"checker": "c230_files_info_data_category", "status": "PASS", "message": "Field 'info.data_category' is found populated with 'Sequencing Reads'. Validation status: PASS"}, {"checker": "c240_submitter_rg_id_collide_with_rg_id_in_bam", "status": "PASS", "message": "For any read group, when 'read_group_id_in_bam' is not populated, 'submitter_read_group_id' must NOT be the same as 'read_group_id_in_bam' of another read group from the same BAM file. Validation result: PASS"}, {"checker": "c250_file_data_type", "status": "PASS", "message": "Field 'dataType' is found populated with 'Submitted Reads'. Validation status: PASS"}, {"checker": "c260_filename_pattern", "status": "PASS", "message": "'fileName' matches expected pattern '^[A-Za-z0-9]{1}[A-Za-z0-9_\\.\\-]*\\.(bam|fq\\.gz|fastq\\.gz|fq\\.bz2|fastq\\.bz2)$' in 'files' section. Validation status: PASS"}, {"checker": "c605_all_files_accessible", "status": "PASS", "message": "All data files accessible check: PASS"}, {"checker": "c608_bam_sanity", "status": "PASS", "message": "BAM sanity check by samtools quickcheck. Validation result: PASS"}, {"checker": "c609_fastq_sanity", "status": "SKIPPED", "message": "This check was not performed as instructed by the command line option. Status: SKIPPED"}, {"checker": "c610_rg_id_in_bam", "status": "PASS", "message": "Read group ID in BAM header check: PASS"}, {"checker": "c620_submitter_read_group_id_match", "status": "PASS", "message": "For each read group, when 'read_group_id_in_bam' is not provided, 'submitter_read_group_id' in the metadata JSON must match RG ID in BAM. Validation result: PASS"}, {"checker": "c630_rg_id_in_bam_match", "status": "PASS", "message": "'read_group_id_in_bam' in metadata matches RG ID in BAM check: PASS"}, {"checker": "c640_one_sm_in_bam_header", "status": "PASS", "message": "One and only one SM in @RG BAM header check: PASS"}, {"checker": "c650_sm_in_bam_matches_metadata", "status": "WARNING", "message": "SM in BAM header is empty. Validation status: WARNING. NOTE that submitterSampleId in metadata JSON will be used in the header of ARGO uniformly aligned sequences."}, {"checker": "c660_metadata_in_bam_rg_header", "status": "WARNING", "message": "Information (excluding ID and SM which are validated elsewhere) in BAM @RG header does NOT match experiment/read group info in the metadata JSON. NOTE that information in the metadata JSON document will be kept and used in ICGC ARGO uniform analysis while unmatched info in BAM header will be discarded. Details of the difference: [BAM anon_chr1_complete.bam @RG QCMG:22f321c6-ff3f-11e4-8e8b-f8a0800c69f0:130711_7001243_0176_BD2B86ACXX.lane_7.CTTGTA.1: (PU: QCMG:130711_7001243_0176_BD2B86ACXX.lane_7.CTTGTA.1 vs QCMG_22f321c6-ff3f-11e4-8e8b-f8a0800c69f0_130711_7001243_0176_BD2B86ACXX.lane_7.CTTGTA.1_8043985)]; [BAM anon_chr1_complete.bam @RG QCMG:866d65b8-ff3f-11e4-b413-bdbd66be296d:130711_7001243_0176_BD2B86ACXX.lane_8.CTTGTA.1: (PU: QCMG:130711_7001243_0176_BD2B86ACXX.lane_8.CTTGTA.1 vs QCMG_866d65b8-ff3f-11e4-b413-bdbd66be296d_130711_7001243_0176_BD2B86ACXX.lane_8.CTTGTA.1_8043985)]; [BAM anon_chr1_complete.bam @RG QCMG:91ce15f2-ff3e-11e4-9d73-85b485b025f8:130711_7001243_0176_BD2B86ACXX.lane_5.CTTGTA.1: (PU: QCMG:130711_7001243_0176_BD2B86ACXX.lane_5.CTTGTA.1 vs QCMG_91ce15f2-ff3e-11e4-9d73-85b485b025f8_130711_7001243_0176_BD2B86ACXX.lane_5.CTTGTA.1_8043985)]; [BAM anon_chr1_complete.bam @RG QCMG:dd3f83b8-ff3e-11e4-81af-910d0943bdb6:130711_7001243_0176_BD2B86ACXX.lane_6.CTTGTA.1: (PU: QCMG:130711_7001243_0176_BD2B86ACXX.lane_6.CTTGTA.1 vs QCMG_dd3f83b8-ff3e-11e4-81af-910d0943bdb6_130711_7001243_0176_BD2B86ACXX.lane_6.CTTGTA.1_8043985)]"}, {"checker": "c670_rg_is_paired_in_bam", "status": "PASS", "message": "Read group pair status in BAM check: PASS"}, {"checker": "c680_repeated_read_names_per_group_in_bam", "status": "PASS", "message": "Repeated Read names within Read groups in BAM not found: PASS"}, {"checker": "c681_fileSize_match", "status": "SKIPPED", "message": "This check was not performed as instructed by the command line option. Status: SKIPPED"}, {"checker": "c683_fileMd5sum_match", "status": "SKIPPED", "message": "This check was not performed as instructed by the command line option. Status: SKIPPED"}]}} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,6 @@ | ||
{ | ||
"json_file": "input/anon_chr1_complete.json", | ||
"files": ["input/anon_chr1_complete.bam"], | ||
"expected_output": "expected/anon_chr1_rnaseq.validation_report.PASS-with-WARNING-and-SKIPPED-check.jsonl", | ||
"skippable_tests" : ["c681","c683","c609"] | ||
} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters