From a86bd74ee1423a6f0205490e6c484f50d14a5105 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Thu, 6 Jul 2023 16:29:47 -0400 Subject: [PATCH 1/6] Update qc_generator --- cwl-commandlinetools | 2 +- cwl_subworkflows | 2 +- qc_generator/nucleo_qc_generator.cwl | 203 ++++++++++++++------------- 3 files changed, 108 insertions(+), 99 deletions(-) diff --git a/cwl-commandlinetools b/cwl-commandlinetools index c8e3cad..14b230b 160000 --- a/cwl-commandlinetools +++ b/cwl-commandlinetools @@ -1 +1 @@ -Subproject commit c8e3cad89655ab5675cd8bcfff97b1c0f8d8a1cd +Subproject commit 14b230bdf44a69ac5b4ec0b312876f4d16e8defc diff --git a/cwl_subworkflows b/cwl_subworkflows index 18a44c5..3e06132 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit 18a44c56e67d0202f565fbf9ac2ec07600e663e7 +Subproject commit 3e06132261bfeeb449fd91eb5e7afe1274ebba9d diff --git a/qc_generator/nucleo_qc_generator.cwl b/qc_generator/nucleo_qc_generator.cwl index 6d013ef..0578561 100644 --- a/qc_generator/nucleo_qc_generator.cwl +++ b/qc_generator/nucleo_qc_generator.cwl @@ -12,27 +12,27 @@ inputs: - ^.fasta.fai - ^.dict 'sbg:x': 0 - 'sbg:y': 1068.28125 + 'sbg:y': 1067.125 - id: duplex_bam type: File label: duplex_bam secondaryFiles: - ^.bai 'sbg:x': 0 - 'sbg:y': 2243.390625 + 'sbg:y': 2561.34375 - id: collapsed_bam type: File label: collapsed_bam secondaryFiles: - ^.bai 'sbg:x': 0 - 'sbg:y': 2563.875 + 'sbg:y': 2881.5 - id: group_reads_by_umi_bam type: File label: group_reads_by_umi_bam doc: Input BAM file generated by GroupReadByUmi. 'sbg:x': 0 - 'sbg:y': 2029.734375 + 'sbg:y': 2134.4140625 - id: uncollapsed_bam_base_recal type: File label: uncollapsed_bam_base_recal @@ -40,17 +40,17 @@ inputs: secondaryFiles: - ^.bai 'sbg:x': 0 - 'sbg:y': 106.828125 + 'sbg:y': 106.703125 - id: target_intervals type: File label: target_intervals 'sbg:x': 0 - 'sbg:y': 213.65625 + 'sbg:y': 213.4296875 - id: bait_intervals type: File label: bait_intervals 'sbg:x': 0 - 'sbg:y': 2884.359375 + 'sbg:y': 3308.359375 - id: noise_sites_bed type: File label: noise_sites_bed @@ -58,87 +58,87 @@ inputs: Path to BED file containing regions over which to calculate noise [required] 'sbg:x': 0 - 'sbg:y': 1175.109375 + 'sbg:y': 1280.53125 - id: sample_sex type: string? doc: Expected sample sex (i.e. M or F). 'sbg:x': 0 - 'sbg:y': 854.625 + 'sbg:y': 853.671875 - id: sample_name type: string? doc: >- Sample name. If not specified, sample name is automatically figured out from the BAM file. - 'sbg:x': 361.90625 - 'sbg:y': 686.9375 + 'sbg:x': 386.90625 + 'sbg:y': 1020.75 - id: sample_group type: string doc: The sample group (e.g. the sample patient ID). 'sbg:x': 0 - 'sbg:y': 961.453125 + 'sbg:y': 960.3984375 - id: simplex_bam type: File label: simplex_bam secondaryFiles: - ^.bai 'sbg:x': 0 - 'sbg:y': 320.484375 + 'sbg:y': 320.15625 - id: biometrics_plot type: boolean? label: biometrics_plot doc: Also output plots of the data. 'sbg:x': 0 - 'sbg:y': 2670.703125 + 'sbg:y': 2988.203125 - id: biometrics_json type: boolean? label: biometrics_json doc: Also output data in JSON format. 'sbg:x': 0 - 'sbg:y': 2777.53125 + 'sbg:y': 3094.9296875 - id: biometrics_bed_file type: File? - 'sbg:x': -423.2972106933594 - 'sbg:y': 2095.491455078125 + 'sbg:x': 0 + 'sbg:y': 3201.65625 - id: collapsed_biometrics_minor_threshold type: float? label: collapsed_biometrics_minor_threshold doc: Minor contamination threshold for bad sample. 'sbg:x': 0 - 'sbg:y': 2350.21875 + 'sbg:y': 2668.046875 - id: collapsed_biometrics_coverage_threshold type: int? label: collapsed_biometrics_coverage_threshold doc: Samples with Y chromosome above this value will be considered male. 'sbg:x': 0 - 'sbg:y': 2457.046875 + 'sbg:y': 2774.7734375 - id: sequence_qc_min_basq type: int? 'sbg:x': 0 - 'sbg:y': 747.796875 + 'sbg:y': 746.96875 - id: sequence_qc_min_mapq type: int? 'sbg:x': 0 - 'sbg:y': 640.96875 + 'sbg:y': 640.265625 - id: sequence_qc_threshold type: float? 'sbg:x': 0 - 'sbg:y': 534.140625 + 'sbg:y': 533.5625 - id: sequence_qc_truncate type: int? 'sbg:x': 0 - 'sbg:y': 427.3125 + 'sbg:y': 426.859375 - id: hsmetrics_minimum_mapping_quality type: int? 'sbg:x': 0 - 'sbg:y': 1602.421875 + 'sbg:y': 1707.4609375 - id: hsmetrics_minimum_base_quality type: int? 'sbg:x': 0 - 'sbg:y': 1709.25 + 'sbg:y': 1814.2109375 - id: hsmetrics_coverage_cap type: int? 'sbg:x': 0 - 'sbg:y': 1816.078125 + 'sbg:y': 1920.9609375 - id: vcf_file type: File 'sbg:x': 0 @@ -146,158 +146,164 @@ inputs: - id: hotspots_maf type: File 'sbg:x': 0 - 'sbg:y': 1922.90625 + 'sbg:y': 2027.6875 - id: mosdepth_bed type: File? - 'sbg:x': -359.3104248046875 - 'sbg:y': 1495 + 'sbg:x': 0 + 'sbg:y': 1600.734375 - id: mosdepth_flag type: int? 'sbg:x': 0 - 'sbg:y': 1388.765625 + 'sbg:y': 1494.0078125 - id: mosdepth_minimum_mapping_quality type: int? 'sbg:x': 0 - 'sbg:y': 1281.9375 + 'sbg:y': 1387.2578125 - id: athena_transcript_file type: File? 'sbg:x': 0 - 'sbg:y': 3098.015625 + 'sbg:y': 3521.765625 - id: athena_build type: File? 'sbg:x': 386.90625 - 'sbg:y': 2556.5625 + 'sbg:y': 2821.171875 - id: athena_flagstat type: File? 'sbg:x': 386.90625 - 'sbg:y': 2342.90625 + 'sbg:y': 2500.9921875 - id: athena_thresholds type: 'int[]?' 'sbg:x': 0 - 'sbg:y': 3204.84375 + 'sbg:y': 3628.46875 - id: athena_threshold type: int? 'sbg:x': 0 - 'sbg:y': 3311.671875 + 'sbg:y': 3735.171875 - id: athena_limit type: int? 'sbg:x': 386.90625 - 'sbg:y': 2236.078125 + 'sbg:y': 2394.265625 - id: athena_summary type: boolean? 'sbg:x': 0 - 'sbg:y': 3418.5 + 'sbg:y': 3841.8984375 - id: athena_vcf type: File? 'sbg:x': 0 - 'sbg:y': 2991.1875 + 'sbg:y': 3415.0625 - id: athena_cores type: int? 'sbg:x': 386.90625 - 'sbg:y': 2449.734375 + 'sbg:y': 2714.46875 - id: output type: 'string[]?' 'sbg:exposed': true - id: omaf type: boolean? + 'sbg:x': 0 + 'sbg:y': 1173.828125 - id: generic_counting type: boolean? + 'sbg:x': 0 + 'sbg:y': 2241.1640625 - id: fragment_count type: int - 'sbg:x': 300.2456970214844 - 'sbg:y': 0 + 'sbg:x': 0 + 'sbg:y': 2347.9140625 - id: filter_duplicate type: int - 'sbg:x': 170.50595092773438 - 'sbg:y': -103.53236389160156 + 'sbg:x': 0 + 'sbg:y': 2454.640625 outputs: - id: uncollapsed_bam_stats_dir outputSource: - uncollapsed_bam_stats/directory type: Directory label: uncollapsed_bam_stats_dir - 'sbg:x': 1625.7747802734375 - 'sbg:y': 1281.9375 + 'sbg:x': 1614.439697265625 + 'sbg:y': 1440.7734375 - id: gatk_mean_quality_by_cycle_recal_dir outputSource: - gatk_mean_quality_by_cycle_recal/directory type: Directory label: gatk_mean_quality_by_cycle_recal_dir - 'sbg:x': 1625.7747802734375 - 'sbg:y': 1495.59375 + 'sbg:x': 1614.439697265625 + 'sbg:y': 1654.203125 - id: collapsed_bam_biometrics_dir outputSource: - collapsed_bam_biometrics/directory type: Directory label: collapsed_bam_biometrics_dir - 'sbg:x': 1625.7747802734375 - 'sbg:y': 2136.5625 + 'sbg:x': 1614.439697265625 + 'sbg:y': 2294.4453125 - id: biometrics_extract_files_dir outputSource: - biometrics_extract_files/directory type: Directory label: biometrics_extract_files_dir - 'sbg:x': 1658.52490234375 - 'sbg:y': 2355.774658203125 + 'sbg:x': 1614.439697265625 + 'sbg:y': 2401.1484375 - id: collapsed_bam_duplex_metrics_dir outputSource: - collapsed_bam_duplex_metrics/directory type: Directory label: collapsed_bam_duplex_metrics_dir - 'sbg:x': 1625.7747802734375 - 'sbg:y': 2029.734375 + 'sbg:x': 1614.439697265625 + 'sbg:y': 2187.7421875 - id: collapsed_bam_stats_dir outputSource: - collapsed_bam_stats/directory type: Directory label: collapsed_bam_stats_dir - 'sbg:x': 1625.7747802734375 - 'sbg:y': 1922.90625 + 'sbg:x': 1614.439697265625 + 'sbg:y': 2081.0390625 - id: simplex_bam_stats_dir outputSource: - simplex_bam_stats/directory type: Directory label: simplex_bam_stats_dir - 'sbg:x': 1625.7747802734375 - 'sbg:y': 1388.765625 + 'sbg:x': 1614.439697265625 + 'sbg:y': 1547.4765625 - id: duplex_bam_sequence_qc_dir outputSource: - duplex_bam_sequence_qc/directory type: Directory label: duplex_bam_sequence_qc_dir - 'sbg:x': 1625.7747802734375 - 'sbg:y': 1709.25 + 'sbg:x': 1614.439697265625 + 'sbg:y': 1867.6328125 - id: duplex_bam_stats_dir outputSource: - duplex_bam_stats/directory type: Directory label: duplex_bam_stats_dir - 'sbg:x': 1625.7747802734375 - 'sbg:y': 1602.421875 + 'sbg:x': 1614.439697265625 + 'sbg:y': 1760.9296875 - id: duplex_bam_biometrics_dir outputSource: - duplex_bam_biometrics/directory type: Directory label: duplex_bam_biometrics_dir - 'sbg:x': 1625.7747802734375 - 'sbg:y': 1816.078125 + 'sbg:x': 1614.439697265625 + 'sbg:y': 1974.3359375 - id: duplex_biometrics_extract_pickle outputSource: - qc_duplex_bam/duplex_biometrics_extract_pickle type: File - 'sbg:x': 1283.092529296875 - 'sbg:y': 1216.3515625 + 'sbg:x': 1276.111572265625 + 'sbg:y': 1428.5 - id: collapsed_biometrics_extract_pickle outputSource: - qc_collapsed_bam/collapsed_biometrics_extract_pickle type: File - 'sbg:x': 1283.092529296875 - 'sbg:y': 1792.4921875 + 'sbg:x': 1276.111572265625 + 'sbg:y': 1897.3125 - id: athena_coverage_report_dir outputSource: - athena_coverage_report/directory type: Directory label: athena_coverage_report_dir + 'sbg:x': 1276.111572265625 + 'sbg:y': 2761.5546875 steps: - id: qc_collapsed_bam in: @@ -317,8 +323,6 @@ 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 @@ -339,6 +343,8 @@ steps: source: sample_group - id: maf source: hotspots_maf + - id: bed_file + source: biometrics_bed_file - id: omaf source: omaf - id: filter_duplicate @@ -376,7 +382,7 @@ steps: run: ../cwl_subworkflows/qc_collapsed_bam/qc_collapsed_bam_v2.0.cwl label: qc_collapsed_bam 'sbg:x': 386.90625 - 'sbg:y': 1975.25 + 'sbg:y': 2133.5625 - id: qc_uncollapsed_bam in: - id: reference @@ -406,7 +412,7 @@ steps: run: ../cwl_subworkflows/qc_uncollapsed_bam/qc_uncollapsed_bam_v2.0.cwl label: qc_uncollapsed_bam 'sbg:x': 386.90625 - 'sbg:y': 1017.765625 + 'sbg:y': 1176.453125 - id: qc_duplex_bam in: - id: reference @@ -492,7 +498,7 @@ steps: run: ../cwl_subworkflows/qc_duplex_bam/qc_duplex_bam_v2.0.cwl label: qc_duplex_bam 'sbg:x': 386.90625 - 'sbg:y': 1539.421875 + 'sbg:y': 1697.859375 - id: athena_report in: - id: transcript_file @@ -511,7 +517,8 @@ steps: - id: sample_name source: sample_name - id: output - source: output + source: + - output - id: limit source: athena_limit - id: summary @@ -529,8 +536,8 @@ steps: - id: coverage_report_single run: ../cwl_subworkflows/athena_report/athena_report.cwl label: athena_report - 'sbg:x': 1382.922119140625 - 'sbg:y': 2798.76611328125 + 'sbg:x': 1276.111572265625 + 'sbg:y': 2570.828125 - id: simplex_bam_stats in: - id: files @@ -549,8 +556,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: simplex_bam_stats - 'sbg:x': 1283.092529296875 - 'sbg:y': 981.6953125 + 'sbg:x': 1276.111572265625 + 'sbg:y': 1194.046875 - id: uncollapsed_bam_stats in: - id: files @@ -569,8 +576,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: uncollapsed_bam_stats - 'sbg:x': 1283.092529296875 - 'sbg:y': 860.8671875 + 'sbg:x': 1276.111572265625 + 'sbg:y': 1073.34375 - id: gatk_mean_quality_by_cycle_recal in: - id: files @@ -586,8 +593,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: gatk_mean_quality_by_cycle_recal - 'sbg:x': 1283.092529296875 - 'sbg:y': 1102.5234375 + 'sbg:x': 1276.111572265625 + 'sbg:y': 1314.7734375 - id: collapsed_bam_stats in: - id: files @@ -607,8 +614,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: collapsed_bam_stats - 'sbg:x': 1283.092529296875 - 'sbg:y': 1906.3203125 + 'sbg:x': 1276.111572265625 + 'sbg:y': 2011.015625 - id: collapsed_bam_duplex_metrics in: - id: files @@ -628,8 +635,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: collapsed_bam_duplex_metrics - 'sbg:x': 1283.092529296875 - 'sbg:y': 2133.9765625 + 'sbg:x': 1276.111572265625 + 'sbg:y': 2131.71875 - id: collapsed_bam_biometrics in: - id: files @@ -654,8 +661,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: collapsed_bam_biometrics - 'sbg:x': 1283.092529296875 - 'sbg:y': 2254.8046875 + 'sbg:x': 1276.111572265625 + 'sbg:y': 2252.421875 - id: biometrics_extract_files in: - id: files @@ -670,8 +677,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: biometrics_extract_files - 'sbg:x': 1290.449951171875 - 'sbg:y': 2410.44970703125 + 'sbg:x': 1276.111572265625 + 'sbg:y': 2373.125 - id: duplex_bam_sequence_qc in: - id: files @@ -691,8 +698,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: duplex_bam_sequence_qc - 'sbg:x': 1283.092529296875 - 'sbg:y': 1451.0078125 + 'sbg:x': 1276.111572265625 + 'sbg:y': 1662.90625 - id: duplex_bam_stats in: - id: files @@ -716,8 +723,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: duplex_bam_stats - 'sbg:x': 1283.092529296875 - 'sbg:y': 1330.1796875 + 'sbg:x': 1276.111572265625 + 'sbg:y': 1542.203125 - id: athena_coverage_report in: - id: files @@ -731,6 +738,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: athena_coverage_report + 'sbg:x': 386.90625 + 'sbg:y': 2607.7421875 - id: duplex_bam_biometrics in: - id: files @@ -747,8 +756,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: duplex_bam_biometrics - 'sbg:x': 1283.092529296875 - 'sbg:y': 1678.6640625 + 'sbg:x': 1276.111572265625 + 'sbg:y': 1783.609375 - id: qc_simplex_bam in: - id: reference @@ -775,7 +784,7 @@ steps: run: ../cwl_subworkflows/qc_simplex_bam/qc_simplex_bam_v2.0.cwl label: qc_simplex_bam 'sbg:x': 386.90625 - 'sbg:y': 1215.59375 + 'sbg:y': 1374.15625 requirements: - class: SubworkflowFeatureRequirement - class: ScatterFeatureRequirement From cd2f695ded90b5c3f1118a2484b8a6109e0c044b Mon Sep 17 00:00:00 2001 From: carmelinacharalambous Date: Thu, 20 Jul 2023 11:58:36 -0400 Subject: [PATCH 2/6] updating nucleo_aggregate_visualize.cwl --- cwl-commandlinetools | 2 +- nucleo_aggregate_visualize.cwl | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cwl-commandlinetools b/cwl-commandlinetools index 14b230b..8c80da0 160000 --- a/cwl-commandlinetools +++ b/cwl-commandlinetools @@ -1 +1 @@ -Subproject commit 14b230bdf44a69ac5b4ec0b312876f4d16e8defc +Subproject commit 8c80da01dbe8d1588e5e000f018828ba48f1b0ed diff --git a/nucleo_aggregate_visualize.cwl b/nucleo_aggregate_visualize.cwl index a0bf18b..0a1213a 100644 --- a/nucleo_aggregate_visualize.cwl +++ b/nucleo_aggregate_visualize.cwl @@ -178,7 +178,7 @@ steps: source: config out: - id: aggregate_parsed_stats - run: cwl-commandlinetools/cci_utils/0.3.0/general_stats_parse.cwl + run: cwl-commandlinetools/cci_utils/0.3.1/general_stats_parse.cwl label: general_stats_parse 'sbg:x': 870.1131591796875 'sbg:y': 520.0625 From 7ef8f9f3739a388dd06a970385c69724dc0db6ba Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Tue, 8 Aug 2023 06:23:54 -0400 Subject: [PATCH 3/6] before publish --- cwl-commandlinetools | 2 +- cwl_subworkflows | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cwl-commandlinetools b/cwl-commandlinetools index 14b230b..cf66cd5 160000 --- a/cwl-commandlinetools +++ b/cwl-commandlinetools @@ -1 +1 @@ -Subproject commit 14b230bdf44a69ac5b4ec0b312876f4d16e8defc +Subproject commit cf66cd5f0269b5a51adceda97c4f5cf046b31133 diff --git a/cwl_subworkflows b/cwl_subworkflows index 3e06132..d9bbc74 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit 3e06132261bfeeb449fd91eb5e7afe1274ebba9d +Subproject commit d9bbc743d68baae2a0372358abaf82e465976b88 From a7e2d5eb8aa2a27201f02761f71e658abb6bca4b Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Tue, 8 Aug 2023 06:27:17 -0400 Subject: [PATCH 4/6] fixing release version --- cwl-commandlinetools | 2 +- cwl_subworkflows | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cwl-commandlinetools b/cwl-commandlinetools index 8c80da0..cf66cd5 160000 --- a/cwl-commandlinetools +++ b/cwl-commandlinetools @@ -1 +1 @@ -Subproject commit 8c80da01dbe8d1588e5e000f018828ba48f1b0ed +Subproject commit cf66cd5f0269b5a51adceda97c4f5cf046b31133 diff --git a/cwl_subworkflows b/cwl_subworkflows index 3e06132..d9bbc74 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit 3e06132261bfeeb449fd91eb5e7afe1274ebba9d +Subproject commit d9bbc743d68baae2a0372358abaf82e465976b88 From 19c8d9911f83727725ee4597d18b57354611e614 Mon Sep 17 00:00:00 2001 From: carmelinacharalambous Date: Tue, 8 Aug 2023 12:46:30 -0400 Subject: [PATCH 5/6] updating working version --- cwl-commandlinetools | 2 +- cwl_subworkflows | 2 +- generate_aggregate.cwl | 3 +- nucleo_qc.cwl | 3 +- qc_generator/nucleo_qc_generator.cwl | 204 +++++++++++++-------------- 5 files changed, 104 insertions(+), 110 deletions(-) diff --git a/cwl-commandlinetools b/cwl-commandlinetools index cf66cd5..8974f3c 160000 --- a/cwl-commandlinetools +++ b/cwl-commandlinetools @@ -1 +1 @@ -Subproject commit cf66cd5f0269b5a51adceda97c4f5cf046b31133 +Subproject commit 8974f3c04d284656f13671a721c8717583d5f756 diff --git a/cwl_subworkflows b/cwl_subworkflows index d9bbc74..c40a063 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit d9bbc743d68baae2a0372358abaf82e465976b88 +Subproject commit c40a06349a395024b68fc11ff9acd3433491fe4f diff --git a/generate_aggregate.cwl b/generate_aggregate.cwl index 7b7cc4d..7c1fa43 100644 --- a/generate_aggregate.cwl +++ b/generate_aggregate.cwl @@ -207,6 +207,7 @@ steps: - id: output source: output - id: omaf + default: true source: omaf - id: generic_counting source: generic_counting @@ -262,7 +263,7 @@ steps: source: - qc_generator/collapsed_bam_stats_dir - id: biometrics_extract_files_dir - source: + source: - qc_generator/biometrics_extract_files_dir - id: collapsed_bam_duplex_metrics_dir source: diff --git a/nucleo_qc.cwl b/nucleo_qc.cwl index 1ad54ab..c17b971 100644 --- a/nucleo_qc.cwl +++ b/nucleo_qc.cwl @@ -230,6 +230,7 @@ steps: - id: output source: output - id: omaf + default: true source: omaf - id: generic_counting source: generic_counting @@ -294,7 +295,7 @@ steps: source: - qc_generator/collapsed_bam_duplex_metrics_dir - id: biometrics_extract_files_dir - source: + source: - qc_generator/biometrics_extract_files_dir - id: samples-json source: samples-json diff --git a/qc_generator/nucleo_qc_generator.cwl b/qc_generator/nucleo_qc_generator.cwl index 0578561..688e14e 100644 --- a/qc_generator/nucleo_qc_generator.cwl +++ b/qc_generator/nucleo_qc_generator.cwl @@ -12,27 +12,27 @@ inputs: - ^.fasta.fai - ^.dict 'sbg:x': 0 - 'sbg:y': 1067.125 + 'sbg:y': 1068.28125 - id: duplex_bam type: File label: duplex_bam secondaryFiles: - ^.bai 'sbg:x': 0 - 'sbg:y': 2561.34375 + 'sbg:y': 2243.390625 - id: collapsed_bam type: File label: collapsed_bam secondaryFiles: - ^.bai 'sbg:x': 0 - 'sbg:y': 2881.5 + 'sbg:y': 2563.875 - id: group_reads_by_umi_bam type: File label: group_reads_by_umi_bam doc: Input BAM file generated by GroupReadByUmi. 'sbg:x': 0 - 'sbg:y': 2134.4140625 + 'sbg:y': 2029.734375 - id: uncollapsed_bam_base_recal type: File label: uncollapsed_bam_base_recal @@ -40,17 +40,17 @@ inputs: secondaryFiles: - ^.bai 'sbg:x': 0 - 'sbg:y': 106.703125 + 'sbg:y': 106.828125 - id: target_intervals type: File label: target_intervals 'sbg:x': 0 - 'sbg:y': 213.4296875 + 'sbg:y': 213.65625 - id: bait_intervals type: File label: bait_intervals 'sbg:x': 0 - 'sbg:y': 3308.359375 + 'sbg:y': 2884.359375 - id: noise_sites_bed type: File label: noise_sites_bed @@ -58,87 +58,87 @@ inputs: Path to BED file containing regions over which to calculate noise [required] 'sbg:x': 0 - 'sbg:y': 1280.53125 + 'sbg:y': 1175.109375 - id: sample_sex type: string? doc: Expected sample sex (i.e. M or F). 'sbg:x': 0 - 'sbg:y': 853.671875 + 'sbg:y': 854.625 - id: sample_name type: string? doc: >- Sample name. If not specified, sample name is automatically figured out from the BAM file. - 'sbg:x': 386.90625 - 'sbg:y': 1020.75 + 'sbg:x': 361.90625 + 'sbg:y': 686.9375 - id: sample_group type: string doc: The sample group (e.g. the sample patient ID). 'sbg:x': 0 - 'sbg:y': 960.3984375 + 'sbg:y': 961.453125 - id: simplex_bam type: File label: simplex_bam secondaryFiles: - ^.bai 'sbg:x': 0 - 'sbg:y': 320.15625 + 'sbg:y': 320.484375 - id: biometrics_plot type: boolean? label: biometrics_plot doc: Also output plots of the data. 'sbg:x': 0 - 'sbg:y': 2988.203125 + 'sbg:y': 2670.703125 - id: biometrics_json type: boolean? label: biometrics_json doc: Also output data in JSON format. 'sbg:x': 0 - 'sbg:y': 3094.9296875 + 'sbg:y': 2777.53125 - id: biometrics_bed_file type: File? - 'sbg:x': 0 - 'sbg:y': 3201.65625 + 'sbg:x': -423.2972106933594 + 'sbg:y': 2095.491455078125 - id: collapsed_biometrics_minor_threshold type: float? label: collapsed_biometrics_minor_threshold doc: Minor contamination threshold for bad sample. 'sbg:x': 0 - 'sbg:y': 2668.046875 + 'sbg:y': 2350.21875 - id: collapsed_biometrics_coverage_threshold type: int? label: collapsed_biometrics_coverage_threshold doc: Samples with Y chromosome above this value will be considered male. 'sbg:x': 0 - 'sbg:y': 2774.7734375 + 'sbg:y': 2457.046875 - id: sequence_qc_min_basq type: int? 'sbg:x': 0 - 'sbg:y': 746.96875 + 'sbg:y': 747.796875 - id: sequence_qc_min_mapq type: int? 'sbg:x': 0 - 'sbg:y': 640.265625 + 'sbg:y': 640.96875 - id: sequence_qc_threshold type: float? 'sbg:x': 0 - 'sbg:y': 533.5625 + 'sbg:y': 534.140625 - id: sequence_qc_truncate type: int? 'sbg:x': 0 - 'sbg:y': 426.859375 + 'sbg:y': 427.3125 - id: hsmetrics_minimum_mapping_quality type: int? 'sbg:x': 0 - 'sbg:y': 1707.4609375 + 'sbg:y': 1602.421875 - id: hsmetrics_minimum_base_quality type: int? 'sbg:x': 0 - 'sbg:y': 1814.2109375 + 'sbg:y': 1709.25 - id: hsmetrics_coverage_cap type: int? 'sbg:x': 0 - 'sbg:y': 1920.9609375 + 'sbg:y': 1816.078125 - id: vcf_file type: File 'sbg:x': 0 @@ -146,164 +146,158 @@ inputs: - id: hotspots_maf type: File 'sbg:x': 0 - 'sbg:y': 2027.6875 + 'sbg:y': 1922.90625 - id: mosdepth_bed type: File? - 'sbg:x': 0 - 'sbg:y': 1600.734375 + 'sbg:x': -359.3104248046875 + 'sbg:y': 1495 - id: mosdepth_flag type: int? 'sbg:x': 0 - 'sbg:y': 1494.0078125 + 'sbg:y': 1388.765625 - id: mosdepth_minimum_mapping_quality type: int? 'sbg:x': 0 - 'sbg:y': 1387.2578125 + 'sbg:y': 1281.9375 - id: athena_transcript_file type: File? 'sbg:x': 0 - 'sbg:y': 3521.765625 + 'sbg:y': 3098.015625 - id: athena_build type: File? 'sbg:x': 386.90625 - 'sbg:y': 2821.171875 + 'sbg:y': 2556.5625 - id: athena_flagstat type: File? 'sbg:x': 386.90625 - 'sbg:y': 2500.9921875 + 'sbg:y': 2342.90625 - id: athena_thresholds type: 'int[]?' 'sbg:x': 0 - 'sbg:y': 3628.46875 + 'sbg:y': 3204.84375 - id: athena_threshold type: int? 'sbg:x': 0 - 'sbg:y': 3735.171875 + 'sbg:y': 3311.671875 - id: athena_limit type: int? 'sbg:x': 386.90625 - 'sbg:y': 2394.265625 + 'sbg:y': 2236.078125 - id: athena_summary type: boolean? 'sbg:x': 0 - 'sbg:y': 3841.8984375 + 'sbg:y': 3418.5 - id: athena_vcf type: File? 'sbg:x': 0 - 'sbg:y': 3415.0625 + 'sbg:y': 2991.1875 - id: athena_cores type: int? 'sbg:x': 386.90625 - 'sbg:y': 2714.46875 + 'sbg:y': 2449.734375 - id: output type: 'string[]?' 'sbg:exposed': true - id: omaf type: boolean? - 'sbg:x': 0 - 'sbg:y': 1173.828125 - id: generic_counting type: boolean? - 'sbg:x': 0 - 'sbg:y': 2241.1640625 - id: fragment_count type: int - 'sbg:x': 0 - 'sbg:y': 2347.9140625 + 'sbg:x': 300.2456970214844 + 'sbg:y': 0 - id: filter_duplicate type: int - 'sbg:x': 0 - 'sbg:y': 2454.640625 + 'sbg:x': 170.50595092773438 + 'sbg:y': -103.53236389160156 outputs: - id: uncollapsed_bam_stats_dir outputSource: - uncollapsed_bam_stats/directory type: Directory label: uncollapsed_bam_stats_dir - 'sbg:x': 1614.439697265625 - 'sbg:y': 1440.7734375 + 'sbg:x': 1625.7747802734375 + 'sbg:y': 1281.9375 - id: gatk_mean_quality_by_cycle_recal_dir outputSource: - gatk_mean_quality_by_cycle_recal/directory type: Directory label: gatk_mean_quality_by_cycle_recal_dir - 'sbg:x': 1614.439697265625 - 'sbg:y': 1654.203125 + 'sbg:x': 1625.7747802734375 + 'sbg:y': 1495.59375 - id: collapsed_bam_biometrics_dir outputSource: - collapsed_bam_biometrics/directory type: Directory label: collapsed_bam_biometrics_dir - 'sbg:x': 1614.439697265625 - 'sbg:y': 2294.4453125 + 'sbg:x': 1625.7747802734375 + 'sbg:y': 2136.5625 - id: biometrics_extract_files_dir outputSource: - biometrics_extract_files/directory type: Directory label: biometrics_extract_files_dir - 'sbg:x': 1614.439697265625 - 'sbg:y': 2401.1484375 + 'sbg:x': 1658.52490234375 + 'sbg:y': 2355.774658203125 - id: collapsed_bam_duplex_metrics_dir outputSource: - collapsed_bam_duplex_metrics/directory type: Directory label: collapsed_bam_duplex_metrics_dir - 'sbg:x': 1614.439697265625 - 'sbg:y': 2187.7421875 + 'sbg:x': 1625.7747802734375 + 'sbg:y': 2029.734375 - id: collapsed_bam_stats_dir outputSource: - collapsed_bam_stats/directory type: Directory label: collapsed_bam_stats_dir - 'sbg:x': 1614.439697265625 - 'sbg:y': 2081.0390625 + 'sbg:x': 1625.7747802734375 + 'sbg:y': 1922.90625 - id: simplex_bam_stats_dir outputSource: - simplex_bam_stats/directory type: Directory label: simplex_bam_stats_dir - 'sbg:x': 1614.439697265625 - 'sbg:y': 1547.4765625 + 'sbg:x': 1625.7747802734375 + 'sbg:y': 1388.765625 - id: duplex_bam_sequence_qc_dir outputSource: - duplex_bam_sequence_qc/directory type: Directory label: duplex_bam_sequence_qc_dir - 'sbg:x': 1614.439697265625 - 'sbg:y': 1867.6328125 + 'sbg:x': 1625.7747802734375 + 'sbg:y': 1709.25 - id: duplex_bam_stats_dir outputSource: - duplex_bam_stats/directory type: Directory label: duplex_bam_stats_dir - 'sbg:x': 1614.439697265625 - 'sbg:y': 1760.9296875 + 'sbg:x': 1625.7747802734375 + 'sbg:y': 1602.421875 - id: duplex_bam_biometrics_dir outputSource: - duplex_bam_biometrics/directory type: Directory label: duplex_bam_biometrics_dir - 'sbg:x': 1614.439697265625 - 'sbg:y': 1974.3359375 + 'sbg:x': 1625.7747802734375 + 'sbg:y': 1816.078125 - id: duplex_biometrics_extract_pickle outputSource: - qc_duplex_bam/duplex_biometrics_extract_pickle type: File - 'sbg:x': 1276.111572265625 - 'sbg:y': 1428.5 + 'sbg:x': 1283.092529296875 + 'sbg:y': 1216.3515625 - id: collapsed_biometrics_extract_pickle outputSource: - qc_collapsed_bam/collapsed_biometrics_extract_pickle type: File - 'sbg:x': 1276.111572265625 - 'sbg:y': 1897.3125 + 'sbg:x': 1283.092529296875 + 'sbg:y': 1792.4921875 - id: athena_coverage_report_dir outputSource: - athena_coverage_report/directory type: Directory label: athena_coverage_report_dir - 'sbg:x': 1276.111572265625 - 'sbg:y': 2761.5546875 steps: - id: qc_collapsed_bam in: @@ -323,6 +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 @@ -343,9 +339,8 @@ steps: source: sample_group - id: maf source: hotspots_maf - - id: bed_file - source: biometrics_bed_file - id: omaf + default: true source: omaf - id: filter_duplicate default: 0 @@ -382,7 +377,7 @@ steps: run: ../cwl_subworkflows/qc_collapsed_bam/qc_collapsed_bam_v2.0.cwl label: qc_collapsed_bam 'sbg:x': 386.90625 - 'sbg:y': 2133.5625 + 'sbg:y': 1975.25 - id: qc_uncollapsed_bam in: - id: reference @@ -412,7 +407,7 @@ steps: run: ../cwl_subworkflows/qc_uncollapsed_bam/qc_uncollapsed_bam_v2.0.cwl label: qc_uncollapsed_bam 'sbg:x': 386.90625 - 'sbg:y': 1176.453125 + 'sbg:y': 1017.765625 - id: qc_duplex_bam in: - id: reference @@ -498,7 +493,7 @@ steps: run: ../cwl_subworkflows/qc_duplex_bam/qc_duplex_bam_v2.0.cwl label: qc_duplex_bam 'sbg:x': 386.90625 - 'sbg:y': 1697.859375 + 'sbg:y': 1539.421875 - id: athena_report in: - id: transcript_file @@ -517,8 +512,7 @@ steps: - id: sample_name source: sample_name - id: output - source: - - output + source: output - id: limit source: athena_limit - id: summary @@ -536,8 +530,8 @@ steps: - id: coverage_report_single run: ../cwl_subworkflows/athena_report/athena_report.cwl label: athena_report - 'sbg:x': 1276.111572265625 - 'sbg:y': 2570.828125 + 'sbg:x': 1382.922119140625 + 'sbg:y': 2798.76611328125 - id: simplex_bam_stats in: - id: files @@ -556,8 +550,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: simplex_bam_stats - 'sbg:x': 1276.111572265625 - 'sbg:y': 1194.046875 + 'sbg:x': 1283.092529296875 + 'sbg:y': 981.6953125 - id: uncollapsed_bam_stats in: - id: files @@ -576,8 +570,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: uncollapsed_bam_stats - 'sbg:x': 1276.111572265625 - 'sbg:y': 1073.34375 + 'sbg:x': 1283.092529296875 + 'sbg:y': 860.8671875 - id: gatk_mean_quality_by_cycle_recal in: - id: files @@ -593,8 +587,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: gatk_mean_quality_by_cycle_recal - 'sbg:x': 1276.111572265625 - 'sbg:y': 1314.7734375 + 'sbg:x': 1283.092529296875 + 'sbg:y': 1102.5234375 - id: collapsed_bam_stats in: - id: files @@ -614,8 +608,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: collapsed_bam_stats - 'sbg:x': 1276.111572265625 - 'sbg:y': 2011.015625 + 'sbg:x': 1283.092529296875 + 'sbg:y': 1906.3203125 - id: collapsed_bam_duplex_metrics in: - id: files @@ -635,8 +629,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: collapsed_bam_duplex_metrics - 'sbg:x': 1276.111572265625 - 'sbg:y': 2131.71875 + 'sbg:x': 1283.092529296875 + 'sbg:y': 2133.9765625 - id: collapsed_bam_biometrics in: - id: files @@ -661,8 +655,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: collapsed_bam_biometrics - 'sbg:x': 1276.111572265625 - 'sbg:y': 2252.421875 + 'sbg:x': 1283.092529296875 + 'sbg:y': 2254.8046875 - id: biometrics_extract_files in: - id: files @@ -677,8 +671,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: biometrics_extract_files - 'sbg:x': 1276.111572265625 - 'sbg:y': 2373.125 + 'sbg:x': 1290.449951171875 + 'sbg:y': 2410.44970703125 - id: duplex_bam_sequence_qc in: - id: files @@ -698,8 +692,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: duplex_bam_sequence_qc - 'sbg:x': 1276.111572265625 - 'sbg:y': 1662.90625 + 'sbg:x': 1283.092529296875 + 'sbg:y': 1451.0078125 - id: duplex_bam_stats in: - id: files @@ -723,8 +717,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: duplex_bam_stats - 'sbg:x': 1276.111572265625 - 'sbg:y': 1542.203125 + 'sbg:x': 1283.092529296875 + 'sbg:y': 1330.1796875 - id: athena_coverage_report in: - id: files @@ -738,8 +732,6 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: athena_coverage_report - 'sbg:x': 386.90625 - 'sbg:y': 2607.7421875 - id: duplex_bam_biometrics in: - id: files @@ -756,8 +748,8 @@ steps: - id: directory run: ../cwl-commandlinetools/expression_tools/put_in_dir.cwl label: duplex_bam_biometrics - 'sbg:x': 1276.111572265625 - 'sbg:y': 1783.609375 + 'sbg:x': 1283.092529296875 + 'sbg:y': 1678.6640625 - id: qc_simplex_bam in: - id: reference @@ -784,7 +776,7 @@ steps: run: ../cwl_subworkflows/qc_simplex_bam/qc_simplex_bam_v2.0.cwl label: qc_simplex_bam 'sbg:x': 386.90625 - 'sbg:y': 1374.15625 + 'sbg:y': 1215.59375 requirements: - class: SubworkflowFeatureRequirement - class: ScatterFeatureRequirement From bd1f169b124e623fdb1a79a78ca229b68559daea Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Tue, 8 Aug 2023 15:21:16 -0400 Subject: [PATCH 6/6] point to release branches --- cwl-commandlinetools | 2 +- cwl_subworkflows | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cwl-commandlinetools b/cwl-commandlinetools index 8974f3c..cf66cd5 160000 --- a/cwl-commandlinetools +++ b/cwl-commandlinetools @@ -1 +1 @@ -Subproject commit 8974f3c04d284656f13671a721c8717583d5f756 +Subproject commit cf66cd5f0269b5a51adceda97c4f5cf046b31133 diff --git a/cwl_subworkflows b/cwl_subworkflows index c40a063..d9bbc74 160000 --- a/cwl_subworkflows +++ b/cwl_subworkflows @@ -1 +1 @@ -Subproject commit c40a06349a395024b68fc11ff9acd3433491fe4f +Subproject commit d9bbc743d68baae2a0372358abaf82e465976b88