From 3a12101f746963e32e7c8e6ceef448b689fc3b71 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Thu, 18 May 2023 09:55:34 -0400 Subject: [PATCH 1/9] Switching back to develop --- cwl-commandlinetools | 2 +- cwl_subworkflows | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cwl-commandlinetools b/cwl-commandlinetools index c8e3cad..939e29b 160000 --- a/cwl-commandlinetools +++ b/cwl-commandlinetools @@ -1 +1 @@ -Subproject commit c8e3cad89655ab5675cd8bcfff97b1c0f8d8a1cd +Subproject commit 939e29be9944d432af9607bfa4eace3e42f55aea diff --git a/cwl_subworkflows b/cwl_subworkflows index 18a44c5..a708e6a 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit 18a44c56e67d0202f565fbf9ac2ec07600e663e7 +Subproject commit a708e6ac1e34218ab960475290a0331f0c60aad4 From 2056f42bd804dca65c07e4c89f06984f7924f1bd Mon Sep 17 00:00:00 2001 From: carmelinacharalambous Date: Thu, 18 May 2023 10:57:09 -0400 Subject: [PATCH 2/9] add missing input biometrics_bed_file --- cwl-commandlinetools | 2 +- cwl_subworkflows | 2 +- qc_generator/nucleo_qc_generator.cwl | 28 +++++++++++++++++++--------- 3 files changed, 21 insertions(+), 11 deletions(-) diff --git a/cwl-commandlinetools b/cwl-commandlinetools index 939e29b..c8e3cad 160000 --- a/cwl-commandlinetools +++ b/cwl-commandlinetools @@ -1 +1 @@ -Subproject commit 939e29be9944d432af9607bfa4eace3e42f55aea +Subproject commit c8e3cad89655ab5675cd8bcfff97b1c0f8d8a1cd diff --git a/cwl_subworkflows b/cwl_subworkflows index a708e6a..1113e53 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit a708e6ac1e34218ab960475290a0331f0c60aad4 +Subproject commit 1113e53155b47c09b61d7f0901ef4db992ec25c8 diff --git a/qc_generator/nucleo_qc_generator.cwl b/qc_generator/nucleo_qc_generator.cwl index d33a9bd..862f15a 100644 --- a/qc_generator/nucleo_qc_generator.cwl +++ b/qc_generator/nucleo_qc_generator.cwl @@ -95,6 +95,10 @@ inputs: doc: Also output data in JSON format. 'sbg:x': 0 'sbg:y': 2777.53125 + - id: biometrics_bed_file + type: File? + 'sbg:x': -423.2972106933594 + 'sbg:y': 2095.491455078125 - id: collapsed_biometrics_minor_threshold type: float? label: collapsed_biometrics_minor_threshold @@ -145,8 +149,8 @@ inputs: 'sbg:y': 1922.90625 - id: mosdepth_bed type: File? - 'sbg:x': 0 - 'sbg:y': 1495.59375 + 'sbg:x': -359.3104248046875 + 'sbg:y': 1495 - id: mosdepth_flag type: int? 'sbg:x': 0 @@ -200,8 +204,12 @@ inputs: type: boolean? - id: fragment_count type: int + 'sbg:x': 300.2456970214844 + 'sbg:y': 0 - id: filter_duplicate type: int + 'sbg:x': 170.50595092773438 + 'sbg:y': -103.53236389160156 outputs: - id: uncollapsed_bam_stats_dir outputSource: @@ -309,6 +317,8 @@ steps: source: biometrics_json - id: plot source: biometrics_plot + - id: bed_file + source: biometrics_bed_file - id: minor_threshold source: collapsed_biometrics_minor_threshold - id: coverage_threshold @@ -329,6 +339,8 @@ steps: source: sample_group - id: maf source: hotspots_maf + - id: bed_file + source: biometrics_bed_file - id: omaf source: omaf - id: filter_duplicate @@ -501,7 +513,8 @@ steps: - id: sample_name source: sample_name - id: output - source: output + source: + - output - id: limit source: athena_limit - id: summary @@ -516,11 +529,11 @@ steps: - id: cores source: athena_cores out: - - id: coverage_report_single + - id: coverage_report run: ../cwl_subworkflows/athena_report/athena_report.cwl label: athena_report - 'sbg:x': 1378 - 'sbg:y': 2784 + 'sbg:x': 1382.922119140625 + 'sbg:y': 2798.76611328125 - id: simplex_bam_stats in: - id: files @@ -768,9 +781,6 @@ steps: 'sbg:y': 1215.59375 requirements: - class: SubworkflowFeatureRequirement - - class: ScatterFeatureRequirement - - class: StepInputExpressionRequirement - - class: InlineJavascriptRequirement - class: MultipleInputFeatureRequirement $schemas: - 'http://schema.org/version/latest/schemaorg-current-http.rdf' From dea98a00a00e07aa307e4a9fc38e6aa21124de1c Mon Sep 17 00:00:00 2001 From: buehlere Date: Thu, 18 May 2023 11:46:34 -0400 Subject: [PATCH 3/9] Update requirements.txt --- requirements.txt | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index 8803225..b9ba408 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,7 +1,6 @@ coloredlogs==15.0.1 pytest==7.2.0 setuptools==65.4.1 -cwltool==3.1.20230425144158 -toil[cwl] @ git+https://github.com/DataBiosphere/toil.git +toil[cwl]==5.10.0 pytest-runner==6.0.0 tox==3.27.1 From b46aa980d8afd322b523215f7f2ce034d2fc97b0 Mon Sep 17 00:00:00 2001 From: carmelinacharalambous Date: Thu, 18 May 2023 15:48:48 -0400 Subject: [PATCH 4/9] qc_generator script working version --- cwl-commandlinetools | 2 +- cwl_subworkflows | 2 +- qc_generator/nucleo_qc_generator.cwl | 7 ++++--- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/cwl-commandlinetools b/cwl-commandlinetools index c8e3cad..939e29b 160000 --- a/cwl-commandlinetools +++ b/cwl-commandlinetools @@ -1 +1 @@ -Subproject commit c8e3cad89655ab5675cd8bcfff97b1c0f8d8a1cd +Subproject commit 939e29be9944d432af9607bfa4eace3e42f55aea diff --git a/cwl_subworkflows b/cwl_subworkflows index 1113e53..a708e6a 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit 1113e53155b47c09b61d7f0901ef4db992ec25c8 +Subproject commit a708e6ac1e34218ab960475290a0331f0c60aad4 diff --git a/qc_generator/nucleo_qc_generator.cwl b/qc_generator/nucleo_qc_generator.cwl index 862f15a..4e52301 100644 --- a/qc_generator/nucleo_qc_generator.cwl +++ b/qc_generator/nucleo_qc_generator.cwl @@ -339,8 +339,6 @@ steps: source: sample_group - id: maf source: hotspots_maf - - id: bed_file - source: biometrics_bed_file - id: omaf source: omaf - id: filter_duplicate @@ -529,7 +527,7 @@ steps: - id: cores source: athena_cores out: - - id: coverage_report + - id: coverage_report_single run: ../cwl_subworkflows/athena_report/athena_report.cwl label: athena_report 'sbg:x': 1382.922119140625 @@ -781,6 +779,9 @@ steps: 'sbg:y': 1215.59375 requirements: - class: SubworkflowFeatureRequirement + - class: ScatterFeatureRequirement + - class: StepInputExpressionRequirement + - class: InlineJavascriptRequirement - class: MultipleInputFeatureRequirement $schemas: - 'http://schema.org/version/latest/schemaorg-current-http.rdf' From 5ed8c92007ac7418125820b05681751ae52799a6 Mon Sep 17 00:00:00 2001 From: carmelinacharalambous Date: Thu, 18 May 2023 16:16:31 -0400 Subject: [PATCH 5/9] subworkflow 1.2.3 --- cwl_subworkflows | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cwl_subworkflows b/cwl_subworkflows index a708e6a..cc32722 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit a708e6ac1e34218ab960475290a0331f0c60aad4 +Subproject commit cc327225c6aa20361c4d2e0b8987f0ac76a42004 From a86d99b2e4e831a4197b7996747f97c489557419 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Fri, 19 May 2023 10:15:29 -0400 Subject: [PATCH 6/9] Update cwl_subworkflows --- cwl_subworkflows | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cwl_subworkflows b/cwl_subworkflows index cc32722..a708e6a 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit cc327225c6aa20361c4d2e0b8987f0ac76a42004 +Subproject commit a708e6ac1e34218ab960475290a0331f0c60aad4 From 631b0905eed1de41f8753d5bff95829a58ca58fa Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Fri, 19 May 2023 10:19:16 -0400 Subject: [PATCH 7/9] Update nucleo_qc_generator.cwl --- qc_generator/nucleo_qc_generator.cwl | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/qc_generator/nucleo_qc_generator.cwl b/qc_generator/nucleo_qc_generator.cwl index 4e52301..6d013ef 100644 --- a/qc_generator/nucleo_qc_generator.cwl +++ b/qc_generator/nucleo_qc_generator.cwl @@ -511,8 +511,7 @@ steps: - id: sample_name source: sample_name - id: output - source: - - output + source: output - id: limit source: athena_limit - id: summary From e0dd6fa3a0067e759176786c23392cc6d38b9beb Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Fri, 19 May 2023 10:22:55 -0400 Subject: [PATCH 8/9] Fixing the vesion of subworkflows --- cwl-commandlinetools | 2 +- cwl_subworkflows | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cwl-commandlinetools b/cwl-commandlinetools index 939e29b..c8e3cad 160000 --- a/cwl-commandlinetools +++ b/cwl-commandlinetools @@ -1 +1 @@ -Subproject commit 939e29be9944d432af9607bfa4eace3e42f55aea +Subproject commit c8e3cad89655ab5675cd8bcfff97b1c0f8d8a1cd diff --git a/cwl_subworkflows b/cwl_subworkflows index a708e6a..18a44c5 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit a708e6ac1e34218ab960475290a0331f0c60aad4 +Subproject commit 18a44c56e67d0202f565fbf9ac2ec07600e663e7 From cb912a2f5b3c4b472263cbc009bb1da4c8edfd66 Mon Sep 17 00:00:00 2001 From: carmelinacharalambous Date: Fri, 19 May 2023 15:55:21 -0400 Subject: [PATCH 9/9] updating main workflows for biometrics_bed_file --- generate_aggregate.cwl | 28 ++++++---------------------- nucleo_qc.cwl | 6 ++++++ 2 files changed, 12 insertions(+), 22 deletions(-) diff --git a/generate_aggregate.cwl b/generate_aggregate.cwl index 81cd537..7b7cc4d 100644 --- a/generate_aggregate.cwl +++ b/generate_aggregate.cwl @@ -26,6 +26,10 @@ inputs: type: File 'sbg:x': 0 'sbg:y': 1813.921875 + - id: biometrics_bed_file + type: File + 'sbg:x': 0 + 'sbg:y': 1813.921875 - id: collapsed_bam type: 'File[]' 'sbg:x': 0 @@ -146,13 +150,6 @@ outputs: type: Directory 'sbg:x': 1585.9033203125 'sbg:y': 1440.421875 - - id: pickle_files_dir - outputSource: - - pickle_files/directory - type: Directory - label: pickle_files_dir - 'sbg:x': 1582 - 'sbg:y': 993 steps: - id: qc_generator in: @@ -182,6 +179,8 @@ steps: source: simplex_bam - id: vcf_file source: biometrics_vcf_file + - id: biometrics_bed_file + source: biometrics_bed_file - id: hotspots_maf source: hotspots_maf - id: mosdepth_bed @@ -286,21 +285,6 @@ steps: label: qc_aggregator 'sbg:x': 1076.5557861328125 'sbg:y': 1270.734375 - - id: pickle_files - in: - - id: files - linkMerge: merge_flattened - source: - - qc_generator/collapsed_biometrics_extract_pickle - - qc_generator/duplex_biometrics_extract_pickle - - id: output_directory_name - default: pickle_files - out: - - id: directory - run: cwl-commandlinetools/expression_tools/put_in_dir.cwl - label: pickle_files - 'sbg:x': 1283.092529296875 - 'sbg:y': 981.6953125 requirements: - class: SubworkflowFeatureRequirement - class: ScatterFeatureRequirement diff --git a/nucleo_qc.cwl b/nucleo_qc.cwl index 04f9b69..1ad54ab 100644 --- a/nucleo_qc.cwl +++ b/nucleo_qc.cwl @@ -28,6 +28,10 @@ inputs: type: File 'sbg:x': 0 'sbg:y': 2030.03125 + - id: biometrics_bed_file + type: File + 'sbg:x': 0 + 'sbg:y': 2030.03125 - id: collapsed_bam type: 'File[]' 'sbg:x': 0 @@ -197,6 +201,8 @@ steps: source: simplex_bam - id: vcf_file source: biometrics_vcf_file + - id: biometrics_bed_file + source: biometrics_bed_file - id: hotspots_maf source: hotspots_maf - id: mosdepth_bed