From 54a0c6a0fab330fa2da41b655648f4602b9aa0e8 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Mon, 18 Feb 2019 12:21:28 +0000 Subject: [PATCH 1/3] remove fastqcheck file generation --- ...2bam_phix_deplex_wtsi_stage1_template.json | 70 ------------------- data/vtlib/subsample.json | 68 ++---------------- 2 files changed, 4 insertions(+), 134 deletions(-) diff --git a/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json b/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json index d1edc4151..cb4c1bab6 100644 --- a/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json +++ b/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json @@ -281,7 +281,6 @@ {"port":"seqchksum", "direction":"out"}, {"port":"spatial_filter", "direction":"out"}, {"port":"subsample", "direction":"out"}, - {"port":"fqc", "direction":"out"}, {"port":"stats", "direction":"out"}, {"port":"split_bam", "direction":"out"}, {"port":"unsplit_bam", "direction":"out"} @@ -367,62 +366,6 @@ "name":{"subst":"run_lane_ss_fqt", "required":true, "ifnull":{"subst_constructor":{ "vals":[ {"subst":"subsetsubpath","default":""}, "/", {"subst":"run_lane_label"}, "_t.fastq" ], "postproc":{"op":"concat","pad":""} } } }, "description":"lane-level fastq output, tagread" }, - { - "id":"bamtofastq_fqc", - "type":"EXEC", - "use_STDIN": true, - "use_STDOUT": true, - "cmd":[ "samtools", - "fastq", - "-F", "0x200", - {"select":"s1_se_pe", "default":"pe", "select_range":[1], "cases":{ - "pe":["-1", {"port":"fq1", "direction":"out"},"-2", {"port":"fq2", "direction":"out"}], - "se":["-0", {"port":"fq1", "direction":"out"}] - }}, - "--i1", {"port":"fqt", "direction":"out"}, - "--index-format", "i99", - "-" - ] - }, - { - "id":"fastqcheck_r1", - "type":"EXEC", - "use_STDIN": true, - "use_STDOUT": true, - "cmd":[ "fastqcheck" ] - }, - { - "id":"fastqcheck_r2", - "type":{"select":"s1_se_pe", "default":"pe", "select_range":[1], "cases":{"pe":"EXEC","se":"INACTIVE"}}, - "use_STDIN": true, - "use_STDOUT": true, - "cmd":[ "fastqcheck" ] - }, - { - "id":"fastqcheck_rt", - "type":"EXEC", - "use_STDIN": true, - "use_STDOUT": true, - "cmd":[ "fastqcheck" ] - }, - { - "id":"fqc1", - "type":"OUTFILE", - "name":{"subst":"fqc1", "required":true, "ifnull":{"subst_constructor":{ "vals":[ {"subst":"outdatadir"}, "/archive/", {"subst":"run_lane_label"}, "_1.fastqcheck" ], "postproc":{"op":"concat","pad":""} } } }, - "description":"lane[1]-level fastqcheck output" - }, - { - "id":"fqc2", - "type":"OUTFILE", - "name":{"subst":"fqc2", "required":true, "ifnull":{"subst_constructor":{ "vals":[ {"subst":"outdatadir"}, "/archive/", {"subst":"run_lane_label"}, "_2.fastqcheck" ], "postproc":{"op":"concat","pad":""} } } }, - "description":"lane[2]-level fastqcheck output" - }, - { - "id":"fqct", - "type":"OUTFILE", - "name":{"subst":"fqct", "required":true, "ifnull":{"subst_constructor":{ "vals":[ {"subst":"outdatadir"}, "/archive/", {"subst":"run_lane_label"}, "_t.fastqcheck" ], "postproc":{"op":"concat","pad":""} } } }, - "description":"lane[t]-level fastqcheck output" - }, { "id":"samtools_stats", "type":"EXEC", @@ -517,19 +460,6 @@ "se":{} }}, { "id":"b2fqss_to_fqt", "from":"bamtofastq_ss:ss_fqt", "to":"run_lane_ss_fqt" }, - { "id":"tee_to_b2fqfqc", "from":"tee_split:fqc", "to":"bamtofastq_fqc" }, - { "id":"fq_to_fqc1", "from":"bamtofastq_fqc:fq1", "to":"fastqcheck_r1" }, - {"select":"s1_se_pe","select_range":[0,1], "default":"pe", "cases":{ - "pe":{ "id":"fq_to_fqc2", "from":"bamtofastq_fqc:fq2", "to":"fastqcheck_r2" }, - "se":{} - }}, - { "id":"fq_to_fqct", "from":"bamtofastq_fqc:fqt", "to":"fastqcheck_rt" }, - { "id":"fqc_to_f1", "from":"fastqcheck_r1", "to":"fqc1" }, - {"select":"s1_se_pe","select_range":[0,1], "default":"pe", "cases":{ - "pe":{ "id":"fqc_to_f2", "from":"fastqcheck_r2", "to":"fqc2" }, - "se":{} - }}, - { "id":"fqc_to_ft", "from":"fastqcheck_rt", "to":"fqct" }, { "id":"tee_to_stats", "from":"tee_split:stats", "to":"samtools_stats" }, { "id":"stats_to_file", "from":"samtools_stats", "to":"lane_stats_file" }, { "id":"stats_to_qc_samtools_stats", "from":"lane_stats_file", "to":"qc_samtools_stats_check" }, diff --git a/data/vtlib/subsample.json b/data/vtlib/subsample.json index 5a91a07b4..a537d1f88 100644 --- a/data/vtlib/subsample.json +++ b/data/vtlib/subsample.json @@ -1,6 +1,6 @@ { "version":"2.0", -"description":"produce 10k subsample fastq files and fastqcheck files", +"description":"produce 10k subsample fastq files", "subgraph_io":{ "ports":{ "inputs":{ @@ -31,8 +31,7 @@ {"subst":"ts_pflag", "ifnull":{"subst":"teepot_pval"}, "comment":"default to no flag; should be set to -p or -P"}, {"port":"straight_through1", "direction":"out"}, {"port":"straight_through2", "direction":"out"}, - {"port":"subsample", "direction":"out"}, - {"port":"fqc", "direction":"out"} + {"port":"subsample", "direction":"out"} ] }, { @@ -73,59 +72,13 @@ "id":"run_lane_ss_fq1", "type":"OUTFILE", "name":{"subst":"run_lane_ss_fq1", "required":true, "ifnull":{"subst_constructor":{ "vals":[ {"subst":"outdatadir"}, "/", {"subst":"subsetsubpath","default":""}, {"subst":"s2_id_run"}, "_", {"subst":"s2_position"}, "_1#", {"subst":"s2_tag_index"}, ".fastq" ], "postproc":{"op":"concat","pad":""} } } }, - "description":"lane-level fastqcheck output, read1" + "description":"lane-level fastq output, read1" }, { "id":"run_lane_ss_fq2", "type":"OUTFILE", "name":{"subst":"run_lane_ss_fq2", "required":true, "ifnull":{"subst_constructor":{ "vals":[ {"subst":"outdatadir"}, "/", {"subst":"subsetsubpath","default":""}, {"subst":"s2_id_run"}, "_", {"subst":"s2_position"}, "_2#", {"subst":"s2_tag_index"}, ".fastq" ], "postproc":{"op":"concat","pad":""} } } }, - "description":"lane-level fastqcheck output, read2" - }, - { - "id":"bamtofastq_fqc", - "type":"EXEC", - "use_STDIN": true, - "use_STDOUT": true, - "cmd":[ "samtools", - "fastq", - "-F", "0x200", - {"select":"s2_se_pe", "default":"pe", "select_range":[1], "cases":{ - "pe":["-1", {"port":"fq1", "direction":"out"},"-2", {"port":"fq2", "direction":"out"}], - "se":["-0", {"port":"fq1", "direction":"out"}] - }}, - "-" - ] - }, - { - "id":"fastqcheck_r1", - "type":"EXEC", - "use_STDIN": true, - "use_STDOUT": true, - "cmd":[ "fastqcheck" ] - }, - {"select":"s2_se_pe", "default":"pe", "select_range":[0,1], "comment":"node only appears if s2_se_pe is pe", - "cases":{ - "pe": - { - "id":"fastqcheck_r2", - "type":"EXEC", - "use_STDIN": true, - "use_STDOUT": true, - "cmd":[ "fastqcheck" ] - }, - "se":{"comment":"fastqcheck_r2 node removed"} - }}, - { - "id":"fqc1", - "type":"OUTFILE", - "name":{"subst":"fqc1", "required":true, "ifnull":{"subst_constructor":{ "vals":[ {"subst":"outdatadir"}, "/", {"subst":"s2_id_run"}, "_", {"subst":"s2_position"}, "_1#", {"subst":"s2_tag_index"}, ".fastqcheck" ], "postproc":{"op":"concat","pad":""} } } }, - "description":"lane[1]-level fastqcheck output" - }, - { - "id":"fqc2", - "type":"OUTFILE", - "name":{"subst":"fqc2", "required":true, "ifnull":{"subst_constructor":{ "vals":[ {"subst":"outdatadir"}, "/", {"subst":"s2_id_run"}, "_", {"subst":"s2_position"}, "_2#", {"subst":"s2_tag_index"}, ".fastqcheck" ], "postproc":{"op":"concat","pad":""} } } }, - "description":"lane[2]-level fastqcheck output" + "description":"lane-level fastq output, read2" } ], "edges":[ @@ -136,19 +89,6 @@ "cases":{ "pe":{ "id":"b2fqss_to_fq2", "from":"bamtofastq_ss:ss_fq2", "to":"run_lane_ss_fq2" }, "se":{"comment":"b2fqss_to_fq2 edge removed"} - }}, - { "id":"tee_to_b2fqfqc", "from":"tee_ssfqc:fqc", "to":"bamtofastq_fqc" }, - { "id":"tee_to_splitter", "from":"bamtofastq_fqc:fq1", "to":"fastqcheck_r1" }, - {"select":"s2_se_pe", "default":"pe", "select_range":[0,1], "comment":"edge only appears if s2_se_pe is pe", - "cases":{ - "pe":{ "id":"bamtofastq_fqx_to_fastqcheck_r2", "from":"bamtofastq_fqc:fq2", "to":"fastqcheck_r2" }, - "se":{"comment":"bamtofastq_fqx_to_fastqcheck_r2 edge removed"} - }}, - { "id":"tee_to_splitter", "from":"fastqcheck_r1", "to":"fqc1" }, - {"select":"s2_se_pe", "default":"pe", "select_range":[0,1], "comment":"edge only appears if s2_se_pe is pe", - "cases":{ - "pe": { "id":"fastqcheck_r2_to_fqc2", "from":"fastqcheck_r2", "to":"fqc2" }, - "se":{"comment":"fastqcheck_r2_to_fqc2 edge removed"} }} ] } From 8c502d9327ce466e61def361a2d2b0091f111ade Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Wed, 6 Mar 2019 15:28:40 +0000 Subject: [PATCH 2/3] remove generation of a fastq file for index read --- data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json | 9 --------- 1 file changed, 9 deletions(-) diff --git a/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json b/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json index cb4c1bab6..dd2aeef3c 100644 --- a/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json +++ b/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json @@ -343,8 +343,6 @@ "pe":["-1", {"port":"ss_fq1", "direction":"out"},"-2", {"port":"ss_fq2", "direction":"out"}], "se":["-0", {"port":"ss_fq1", "direction":"out"}] }}, - "--i1", {"port":"ss_fqt", "direction":"out"}, - "--index-format", "i99", "-" ] }, @@ -360,12 +358,6 @@ "name":{"subst":"run_lane_ss_fq2", "required":true, "ifnull":{"subst_constructor":{ "vals":[ {"subst":"subsetsubpath","default":""}, "/", {"subst":"run_lane_label"}, "_2.fastq" ], "postproc":{"op":"concat","pad":""} } } }, "description":"lane-level fastq output, read2" }, - { - "id":"run_lane_ss_fqt", - "type":"OUTFILE", - "name":{"subst":"run_lane_ss_fqt", "required":true, "ifnull":{"subst_constructor":{ "vals":[ {"subst":"subsetsubpath","default":""}, "/", {"subst":"run_lane_label"}, "_t.fastq" ], "postproc":{"op":"concat","pad":""} } } }, - "description":"lane-level fastq output, tagread" - }, { "id":"samtools_stats", "type":"EXEC", @@ -459,7 +451,6 @@ "pe":{"id":"b2fqss_to_fq2", "from":"bamtofastq_ss:ss_fq2", "to":"run_lane_ss_fq2"}, "se":{} }}, - { "id":"b2fqss_to_fqt", "from":"bamtofastq_ss:ss_fqt", "to":"run_lane_ss_fqt" }, { "id":"tee_to_stats", "from":"tee_split:stats", "to":"samtools_stats" }, { "id":"stats_to_file", "from":"samtools_stats", "to":"lane_stats_file" }, { "id":"stats_to_qc_samtools_stats", "from":"lane_stats_file", "to":"qc_samtools_stats_check" }, From 08439e58756052236e5bb9f2bb71ef581d6a0e62 Mon Sep 17 00:00:00 2001 From: mgcam Date: Tue, 12 Mar 2019 14:20:33 +0000 Subject: [PATCH 3/3] changes file update for release 0.24.2 --- Changes | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/Changes b/Changes index 20e7e9797..02f05b323 100644 --- a/Changes +++ b/Changes @@ -1,5 +1,9 @@ CHANGES LOG ----------- +release 0.24.2 + - stage 1 and seq alignment templates: remove fastqcheck file generation + - stage 1 template: remove generation of a fastq file for index read + release 0.24.1 - correct count of minimum reads to run Salmon