From 4bbec1eb9807fcf0f161ef7faeae22a60239c825 Mon Sep 17 00:00:00 2001 From: voyager pipeline user Date: Fri, 29 Sep 2023 16:15:59 +0000 Subject: [PATCH 01/19] fixing format fo chipvar subworkflow dates --- variant_annotation/variant_annotation.cwl | 0 variant_postprocessing/variants_concat.cwl | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) mode change 100644 => 100755 variant_annotation/variant_annotation.cwl mode change 100644 => 100755 variant_postprocessing/variants_concat.cwl diff --git a/variant_annotation/variant_annotation.cwl b/variant_annotation/variant_annotation.cwl old mode 100644 new mode 100755 diff --git a/variant_postprocessing/variants_concat.cwl b/variant_postprocessing/variants_concat.cwl old mode 100644 new mode 100755 index ba80de4..1aad408 --- a/variant_postprocessing/variants_concat.cwl +++ b/variant_postprocessing/variants_concat.cwl @@ -161,5 +161,5 @@ $schemas: 's:email': 'mailto:shahr@mskcc.org' 's:identifier': '' 's:name': Ronak Shah -'s:dateCreated': 2020-07-13 +'s:dateCreated': '2020-07-13' 's:license': 'https://spdx.org/licenses/Apache-2.0' From 9480c0b66bbf7ab46cc932dc2662a86f41ff63bf Mon Sep 17 00:00:00 2001 From: Karthigayini Sivaprakasam Date: Tue, 26 Dec 2023 14:14:52 -0600 Subject: [PATCH 02/19] variant annotation - image change --- .gitignore | 1 + command_line_tools | 2 +- variant_annotation/variant_annotation.cwl | 162 +++++++++++----------- 3 files changed, 86 insertions(+), 79 deletions(-) diff --git a/.gitignore b/.gitignore index 6df9a5f..5e53842 100644 --- a/.gitignore +++ b/.gitignore @@ -107,3 +107,4 @@ ENV/ #vscode .vscode/* +pv_vardict/pv_maf_processing.cwl diff --git a/command_line_tools b/command_line_tools index cf66cd5..658de77 160000 --- a/command_line_tools +++ b/command_line_tools @@ -1 +1 @@ -Subproject commit cf66cd5f0269b5a51adceda97c4f5cf046b31133 +Subproject commit 658de774e792d65668de9becb7e8a18775723534 diff --git a/variant_annotation/variant_annotation.cwl b/variant_annotation/variant_annotation.cwl index b59225b..69a08df 100755 --- a/variant_annotation/variant_annotation.cwl +++ b/variant_annotation/variant_annotation.cwl @@ -11,114 +11,120 @@ inputs: secondaryFiles: - .tbi 'sbg:x': 0 - 'sbg:y': 434.1875 + 'sbg:y': 855.25 - id: vardict_input_vcf type: File 'sbg:x': 0 - 'sbg:y': 327.390625 + 'sbg:y': 0 - id: input_cosmicprevalenceDB_vcf type: File secondaryFiles: - .tbi - 'sbg:x': 217.47328186035156 - 'sbg:y': 564.6259765625 + 'sbg:x': 272.546875 + 'sbg:y': 481.078125 - id: min_hom_vaf type: float? - 'sbg:x': 416.7921447753906 - 'sbg:y': 654.78125 + 'sbg:x': 573.796875 + 'sbg:y': 601.984375 - id: output_vcf2mafName type: string? - 'sbg:x': 416.7921447753906 - 'sbg:y': 441.1875 + 'sbg:x': 573.796875 + 'sbg:y': 495.078125 - id: retain_info type: string? - 'sbg:x': 407 - 'sbg:y': 277 + 'sbg:x': 573.796875 + 'sbg:y': 388.171875 - id: tumor_id type: string? - 'sbg:x': 469 - 'sbg:y': -64 + 'sbg:x': 573.796875 + 'sbg:y': 146.359375 - id: snpsift_countOpName type: string? - 'sbg:x': 16.4202823638916 - 'sbg:y': 169.89190673828125 + 'sbg:x': 0 + 'sbg:y': 213.8125 - id: snpsift_prevalOpName type: string? - 'sbg:x': 214.9839324951172 - 'sbg:y': -51.58765411376953 + 'sbg:x': 0 + 'sbg:y': 106.90625 - id: opOncoKbMafName type: string - 'sbg:x': 953.6817626953125 - 'sbg:y': 129.14283752441406 + 'sbg:x': 0 + 'sbg:y': 534.53125 - id: oncoKbApiToken type: File - 'sbg:x': 934 - 'sbg:y': 402 + 'sbg:x': 0 + 'sbg:y': 641.4375 - id: oncoKbAnnotateHotspots type: boolean? - 'sbg:x': 914.09375 - 'sbg:y': 582.5 - - id: input_mappability_bed + 'sbg:x': 0 + 'sbg:y': 748.34375 + - id: input_mapabbility_bed type: File - 'sbg:x': 1137.1201171875 - 'sbg:y': 407.4906311035156 - - id: output_mappability_filename - type: string? - 'sbg:x': 1172.9835205078125 - 'sbg:y': 68.39226531982422 - - id: column_name_mappability - type: string? - 'sbg:x': 1273.205322265625 - 'sbg:y': 514.48193359375 + 'sbg:x': 1163.603759765625 + 'sbg:y': 502.078125 - id: input_complexity_bed type: File - 'sbg:x': 1455.4620361328125 - 'sbg:y': 427.4315490722656 - - id: column_name_complexity + 'sbg:x': 1428.8468017578125 + 'sbg:y': 502.078125 + - id: output_mapability_filename + type: string + 'sbg:x': 0 + 'sbg:y': 320.71875 + - id: column_name_mapability type: string? - 'sbg:x': 1688.9140625 - 'sbg:y': 449.50762939453125 + 'sbg:x': 1163.603759765625 + 'sbg:y': 608.984375 - id: output_complexity_filename + type: string + 'sbg:x': 0 + 'sbg:y': 427.625 + - id: column_name_complexity type: string? - 'sbg:x': 1609.2314453125 - 'sbg:y': 21.32272720336914 + 'sbg:x': 1428.8468017578125 + 'sbg:y': 608.984375 outputs: - id: cosmicCount_annotatedOutput outputSource: - snpsift_annotate_5_0/annotatedOutput type: File - 'sbg:x': 348.4152526855469 - 'sbg:y': 772.9266967773438 + 'sbg:x': 573.796875 + 'sbg:y': 708.890625 - id: annotatedOutput_prevalence outputSource: - snpsift_annotate_5_1/annotatedOutput type: File - 'sbg:x': 656.337158203125 - 'sbg:y': 723.7005615234375 + 'sbg:x': 871.65625 + 'sbg:y': 481.078125 - id: vcf2maf_maf outputSource: - vcf2maf_v1_6_21/vcf2maf_maf type: File - 'sbg:x': 1148.8089599609375 - 'sbg:y': 594.5475463867188 - - id: output_mappability_maf + 'sbg:x': 1163.603759765625 + 'sbg:y': 246.265625 + - id: oncokb_maf + outputSource: + - oncokb_annotator/outputMaf + type: File? + 'sbg:x': 1428.8468017578125 + 'sbg:y': 246.265625 + - id: output_mapability_maf outputSource: - - maf_annotated_by_bed_mappability/output + - maf_annotated_by_bed/output type: File - 'sbg:x': 1524.598876953125 - 'sbg:y': 679.8934936523438 + 'sbg:x': 1686.1904296875 + 'sbg:y': 353.171875 - id: output_complexity_maf outputSource: - - maf_annotated_by_bed_lowComplexity/output + - maf_annotated_by_bed_1/output type: File - 'sbg:x': 1815.8809814453125 - 'sbg:y': 248.1118621826172 - - id: oncokb_maf + 'sbg:x': 1923.05859375 + 'sbg:y': 374.171875 + - id: output outputSource: - - oncokb_annotator/outputMaf - type: File? - 'sbg:x': 1327.9454345703125 - 'sbg:y': 738.3821411132812 + - maf_annotated_by_bed_1/output + type: File + 'sbg:x': 1923.05859375 + 'sbg:y': 481.078125 steps: - id: snpsift_annotate_5_0 in: @@ -132,8 +138,8 @@ steps: - id: annotatedOutput run: ../command_line_tools/snpsift_annotate_5.0/snpsift_annotate_5-0.cwl label: snpsift_countAnnotation - 'sbg:x': 155.640625 - 'sbg:y': 320.390625 + 'sbg:x': 272.546875 + 'sbg:y': 360.171875 - id: snpsift_annotate_5_1 in: - id: input_DB_vcf @@ -146,8 +152,8 @@ steps: - id: annotatedOutput run: ../command_line_tools/snpsift_annotate_5.0/snpsift_annotate_5-0.cwl label: snpsift_annotate_5.0 - 'sbg:x': 416.7921447753906 - 'sbg:y': 113.796875 + 'sbg:x': 573.796875 + 'sbg:y': 267.265625 - id: vcf2maf_v1_6_21 in: - id: input_vcf @@ -171,8 +177,8 @@ steps: out: - id: vcf2maf_maf run: ../command_line_tools//vcf2maf_1.6.21/vcf2maf_1.6.21.cwl - 'sbg:x': 833.5098266601562 - 'sbg:y': 276.9501953125 + 'sbg:x': 871.65625 + 'sbg:y': 339.171875 - id: oncokb_annotator in: - id: inputMafFile @@ -189,29 +195,29 @@ steps: - id: outputMaf run: ../command_line_tools/oncokb_annotator_3.2.2/oncokb_annotator_3-2-2.cwl label: oncokb_annotator - 'sbg:x': 1096.5919189453125 - 'sbg:y': 261 - - id: maf_annotated_by_bed_mappability + 'sbg:x': 1163.603759765625 + 'sbg:y': 374.171875 + - id: maf_annotated_by_bed in: - id: input_maf source: oncokb_annotator/outputMaf - id: input_bed - source: input_mappability_bed + source: input_mapabbility_bed - id: output_filename - source: output_mappability_filename + source: output_mapability_filename - id: column_name - source: column_name_mappability + source: column_name_mapability out: - id: output run: >- - ../command_line_tools/postprocessing_variant_calls/0.2.2/maf_annotated_by_bed/maf_annotated_by_bed.cwl + ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_annotated_by_bed/maf_annotated_by_bed.cwl label: maf_annotated_by_bed - 'sbg:x': 1317.3984375 - 'sbg:y': 267 - - id: maf_annotated_by_bed_lowComplexity + 'sbg:x': 1428.8468017578125 + 'sbg:y': 374.171875 + - id: maf_annotated_by_bed_1 in: - id: input_maf - source: maf_annotated_by_bed_mappability/output + source: maf_annotated_by_bed/output - id: input_bed source: input_complexity_bed - id: output_filename @@ -221,10 +227,10 @@ steps: out: - id: output run: >- - ../command_line_tools/postprocessing_variant_calls/0.2.2/maf_annotated_by_bed/maf_annotated_by_bed.cwl + ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_annotated_by_bed/maf_annotated_by_bed.cwl label: maf_annotated_by_bed - 'sbg:x': 1600 - 'sbg:y': 262.8888854980469 + 'sbg:x': 1748.00244140625 + 'sbg:y': 573.7960815429688 requirements: [] $schemas: - 'http://schema.org/version/latest/schemaorg-current-http.rdf' From 45b70924233437af49689b20b31b286d1d063a36 Mon Sep 17 00:00:00 2001 From: Karthigayini Sivaprakasam Date: Tue, 26 Dec 2023 17:10:13 -0600 Subject: [PATCH 03/19] spellings --- variant_annotation/variant_annotation.cwl | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/variant_annotation/variant_annotation.cwl b/variant_annotation/variant_annotation.cwl index 69a08df..a436367 100755 --- a/variant_annotation/variant_annotation.cwl +++ b/variant_annotation/variant_annotation.cwl @@ -58,7 +58,7 @@ inputs: type: boolean? 'sbg:x': 0 'sbg:y': 748.34375 - - id: input_mapabbility_bed + - id: input_mappability_bed type: File 'sbg:x': 1163.603759765625 'sbg:y': 502.078125 @@ -66,11 +66,11 @@ inputs: type: File 'sbg:x': 1428.8468017578125 'sbg:y': 502.078125 - - id: output_mapability_filename + - id: output_mappability_filename type: string 'sbg:x': 0 'sbg:y': 320.71875 - - id: column_name_mapability + - id: column_name_mappability type: string? 'sbg:x': 1163.603759765625 'sbg:y': 608.984375 @@ -202,18 +202,18 @@ steps: - id: input_maf source: oncokb_annotator/outputMaf - id: input_bed - source: input_mapabbility_bed + source: input_mappability_bed - id: output_filename - source: output_mapability_filename + source: output_mappability_filename - id: column_name - source: column_name_mapability + source: column_name_mappability out: - id: output run: >- ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_annotated_by_bed/maf_annotated_by_bed.cwl label: maf_annotated_by_bed - 'sbg:x': 1428.8468017578125 - 'sbg:y': 374.171875 + 'sbg:x': 1464.233642578125 + 'sbg:y': 372.9342956542969 - id: maf_annotated_by_bed_1 in: - id: input_maf From 116652b138291f81dd9cf245c8bffc2ada4fe856 Mon Sep 17 00:00:00 2001 From: Karthigayini Sivaprakasam Date: Wed, 27 Dec 2023 11:50:29 -0600 Subject: [PATCH 04/19] chipvar tagging added --- variant_annotation/variant_annotation.cwl | 225 ++++++++++++++++------ 1 file changed, 165 insertions(+), 60 deletions(-) diff --git a/variant_annotation/variant_annotation.cwl b/variant_annotation/variant_annotation.cwl index a436367..246d1ed 100755 --- a/variant_annotation/variant_annotation.cwl +++ b/variant_annotation/variant_annotation.cwl @@ -10,91 +10,127 @@ inputs: type: File secondaryFiles: - .tbi - 'sbg:x': 0 - 'sbg:y': 855.25 + 'sbg:x': 23.445261001586914 + 'sbg:y': 364.7808837890625 - id: vardict_input_vcf type: File - 'sbg:x': 0 - 'sbg:y': 0 + 'sbg:x': -6.394162178039551 + 'sbg:y': 252.5694122314453 - id: input_cosmicprevalenceDB_vcf type: File secondaryFiles: - .tbi - 'sbg:x': 272.546875 - 'sbg:y': 481.078125 + 'sbg:x': 478.74456787109375 + 'sbg:y': 357.3795166015625 - id: min_hom_vaf type: float? - 'sbg:x': 573.796875 - 'sbg:y': 601.984375 + 'sbg:x': 811.7153930664062 + 'sbg:y': 475.2481384277344 - id: output_vcf2mafName type: string? - 'sbg:x': 573.796875 - 'sbg:y': 495.078125 + 'sbg:x': 810.6497192382812 + 'sbg:y': 390.56201171875 - id: retain_info type: string? - 'sbg:x': 573.796875 - 'sbg:y': 388.171875 + 'sbg:x': 833.029296875 + 'sbg:y': 255.85397338867188 - id: tumor_id type: string? - 'sbg:x': 573.796875 - 'sbg:y': 146.359375 + 'sbg:x': 876.7227172851562 + 'sbg:y': 144.93431091308594 - id: snpsift_countOpName type: string? - 'sbg:x': 0 - 'sbg:y': 213.8125 + 'sbg:x': 21.313875198364258 + 'sbg:y': 146.92698669433594 - id: snpsift_prevalOpName type: string? - 'sbg:x': 0 - 'sbg:y': 106.90625 + 'sbg:x': 471.03662109375 + 'sbg:y': 208.3065948486328 - id: opOncoKbMafName type: string - 'sbg:x': 0 - 'sbg:y': 534.53125 + 'sbg:x': 1262.8470458984375 + 'sbg:y': 271.8393249511719 - id: oncoKbApiToken type: File - 'sbg:x': 0 - 'sbg:y': 641.4375 + 'sbg:x': 1170.1317138671875 + 'sbg:y': 455.5693054199219 - id: oncoKbAnnotateHotspots type: boolean? - 'sbg:x': 0 - 'sbg:y': 748.34375 + 'sbg:x': 1230.876220703125 + 'sbg:y': 542.3211059570312 - id: input_mappability_bed type: File - 'sbg:x': 1163.603759765625 - 'sbg:y': 502.078125 + 'sbg:x': 1663.8760986328125 + 'sbg:y': 483.8832092285156 - id: input_complexity_bed type: File - 'sbg:x': 1428.8468017578125 - 'sbg:y': 502.078125 + 'sbg:x': 1974.700927734375 + 'sbg:y': 498.8029479980469 - id: output_mappability_filename type: string - 'sbg:x': 0 - 'sbg:y': 320.71875 + 'sbg:x': 1618.7889404296875 + 'sbg:y': 318.9342956542969 - id: column_name_mappability type: string? - 'sbg:x': 1163.603759765625 - 'sbg:y': 608.984375 + 'sbg:x': 1702.2410888671875 + 'sbg:y': 577.0948486328125 - id: output_complexity_filename type: string - 'sbg:x': 0 - 'sbg:y': 427.625 + 'sbg:x': 2086.625732421875 + 'sbg:y': 382.24090576171875 - id: column_name_complexity type: string? - 'sbg:x': 1428.8468017578125 - 'sbg:y': 608.984375 + 'sbg:x': 2012.0001220703125 + 'sbg:y': 601.6058349609375 + - id: input_hotspot_tsv_file + type: File + 'sbg:x': 2425.953857421875 + 'sbg:y': 306.6236572265625 + - id: output_column_name_hotpsot + type: string? + 'sbg:x': 2538.91748046875 + 'sbg:y': 206.44845581054688 + - id: output_hotspot_maf_name + type: string? + 'sbg:x': 2457.218994140625 + 'sbg:y': 758.5621337890625 + - id: input_47kchpd_tsv_file + type: File + 'sbg:x': 2759.510498046875 + 'sbg:y': 265.0616149902344 + - id: output_47kchpd_maf_name + type: string? + 'sbg:x': 3004.045654296875 + 'sbg:y': 208.01800537109375 + - id: output_column_name_47kchpd + type: string? + 'sbg:x': 2837.483642578125 + 'sbg:y': 590.1929931640625 + - id: input_panmeloid_tsv_file + type: File + 'sbg:x': 3165.773193359375 + 'sbg:y': 219.0523681640625 + - id: output_maf_name_panmyeloid + type: string? + 'sbg:x': 3330.037841796875 + 'sbg:y': 199.72714233398438 + - id: output_column_name_panmyeloid + type: string? + 'sbg:x': 3216.4921875 + 'sbg:y': 559.9721069335938 outputs: - id: cosmicCount_annotatedOutput outputSource: - snpsift_annotate_5_0/annotatedOutput type: File - 'sbg:x': 573.796875 - 'sbg:y': 708.890625 + 'sbg:x': 224.51815795898438 + 'sbg:y': 602.496337890625 - id: annotatedOutput_prevalence outputSource: - snpsift_annotate_5_1/annotatedOutput type: File - 'sbg:x': 871.65625 - 'sbg:y': 481.078125 + 'sbg:x': 714.343017578125 + 'sbg:y': 463.94891357421875 - id: vcf2maf_maf outputSource: - vcf2maf_v1_6_21/vcf2maf_maf @@ -105,26 +141,44 @@ outputs: outputSource: - oncokb_annotator/outputMaf type: File? - 'sbg:x': 1428.8468017578125 - 'sbg:y': 246.265625 + 'sbg:x': 1504.72998046875 + 'sbg:y': 733.0220336914062 - id: output_mapability_maf outputSource: - maf_annotated_by_bed/output type: File - 'sbg:x': 1686.1904296875 - 'sbg:y': 353.171875 + 'sbg:x': 2008.9051513671875 + 'sbg:y': 272.00726318359375 - id: output_complexity_maf outputSource: - maf_annotated_by_bed_1/output type: File - 'sbg:x': 1923.05859375 - 'sbg:y': 374.171875 + 'sbg:x': 2283.204345703125 + 'sbg:y': 275.9561767578125 - id: output outputSource: - maf_annotated_by_bed_1/output type: File - 'sbg:x': 1923.05859375 - 'sbg:y': 481.078125 + 'sbg:x': 2380.1826171875 + 'sbg:y': 616.3430786132812 + - id: output_hotspot_maf + outputSource: + - pv_maf_annotated_by_tsv/output + type: File? + 'sbg:x': 2793.349609375 + 'sbg:y': 755.3427734375 + - id: output_47kchpd_maf + outputSource: + - pv_maf_annotated_by_tsv_1/output + type: File? + 'sbg:x': 3171.963623046875 + 'sbg:y': 695.1704711914062 + - id: output_panmyeloid_maf + outputSource: + - pv_maf_annotated_by_tsv_2/output + type: File? + 'sbg:x': 3498.328369140625 + 'sbg:y': 604.7518310546875 steps: - id: snpsift_annotate_5_0 in: @@ -138,8 +192,8 @@ steps: - id: annotatedOutput run: ../command_line_tools/snpsift_annotate_5.0/snpsift_annotate_5-0.cwl label: snpsift_countAnnotation - 'sbg:x': 272.546875 - 'sbg:y': 360.171875 + 'sbg:x': 245.35765075683594 + 'sbg:y': 251.2992401123047 - id: snpsift_annotate_5_1 in: - id: input_DB_vcf @@ -152,8 +206,8 @@ steps: - id: annotatedOutput run: ../command_line_tools/snpsift_annotate_5.0/snpsift_annotate_5-0.cwl label: snpsift_annotate_5.0 - 'sbg:x': 573.796875 - 'sbg:y': 267.265625 + 'sbg:x': 639.072998046875 + 'sbg:y': 278.7226257324219 - id: vcf2maf_v1_6_21 in: - id: input_vcf @@ -177,8 +231,8 @@ steps: out: - id: vcf2maf_maf run: ../command_line_tools//vcf2maf_1.6.21/vcf2maf_1.6.21.cwl - 'sbg:x': 871.65625 - 'sbg:y': 339.171875 + 'sbg:x': 1015.934326171875 + 'sbg:y': 356.05108642578125 - id: oncokb_annotator in: - id: inputMafFile @@ -195,8 +249,8 @@ steps: - id: outputMaf run: ../command_line_tools/oncokb_annotator_3.2.2/oncokb_annotator_3-2-2.cwl label: oncokb_annotator - 'sbg:x': 1163.603759765625 - 'sbg:y': 374.171875 + 'sbg:x': 1426.226318359375 + 'sbg:y': 402.77374267578125 - id: maf_annotated_by_bed in: - id: input_maf @@ -212,8 +266,8 @@ steps: run: >- ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_annotated_by_bed/maf_annotated_by_bed.cwl label: maf_annotated_by_bed - 'sbg:x': 1464.233642578125 - 'sbg:y': 372.9342956542969 + 'sbg:x': 1838.0584716796875 + 'sbg:y': 425.2846984863281 - id: maf_annotated_by_bed_1 in: - id: input_maf @@ -229,8 +283,59 @@ steps: run: >- ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_annotated_by_bed/maf_annotated_by_bed.cwl label: maf_annotated_by_bed - 'sbg:x': 1748.00244140625 - 'sbg:y': 573.7960815429688 + 'sbg:x': 2220.102294921875 + 'sbg:y': 478.15325927734375 + - id: pv_maf_annotated_by_tsv + in: + - id: input_maf + source: maf_annotated_by_bed_1/output + - id: output_maf_name + source: output_hotspot_maf_name + - id: output_column_name + source: output_column_name_hotpsot + - id: input_tsv_file + source: input_hotspot_tsv_file + out: + - id: output + run: >- + ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_annotate_by_tsv/maf_annotate_by_tsv.cwl + label: pv_maf_annotatedByTsv + 'sbg:x': 2624.56201171875 + 'sbg:y': 446.36090087890625 + - id: pv_maf_annotated_by_tsv_1 + in: + - id: input_maf + source: pv_maf_annotated_by_tsv/output + - id: output_maf_name + source: output_47kchpd_maf_name + - id: output_column_name + source: output_column_name_47kchpd + - id: input_tsv_file + source: input_47kchpd_tsv_file + out: + - id: output + run: >- + ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_annotate_by_tsv/maf_annotate_by_tsv.cwl + label: pv_maf_annotatedByTsv + 'sbg:x': 3027.093994140625 + 'sbg:y': 444.81915283203125 + - id: pv_maf_annotated_by_tsv_2 + in: + - id: input_maf + source: pv_maf_annotated_by_tsv_1/output + - id: output_maf_name + source: output_maf_name_panmyeloid + - id: output_column_name + source: output_column_name_panmyeloid + - id: input_tsv_file + source: input_panmeloid_tsv_file + out: + - id: output + run: >- + ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_annotate_by_tsv/maf_annotate_by_tsv.cwl + label: pv_maf_annotatedByTsv + 'sbg:x': 3366.108154296875 + 'sbg:y': 434.5843505859375 requirements: [] $schemas: - 'http://schema.org/version/latest/schemaorg-current-http.rdf' From c021507f4513020ac2199343a79ffd0c675e02cc Mon Sep 17 00:00:00 2001 From: Karthigayini Sivaprakasam Date: Wed, 27 Dec 2023 15:38:09 -0600 Subject: [PATCH 05/19] chipvar psot processing --- variant_annotation/chipvar_processing.cwl | 60 +++++++++++++++++++ .../example_inputs_chipvar.yaml | 5 ++ ...=> example_inputs_variant_annotation.yaml} | 0 3 files changed, 65 insertions(+) create mode 100644 variant_annotation/chipvar_processing.cwl create mode 100644 variant_annotation/example_inputs_chipvar.yaml rename variant_annotation/{example_inputs.yaml => example_inputs_variant_annotation.yaml} (100%) diff --git a/variant_annotation/chipvar_processing.cwl b/variant_annotation/chipvar_processing.cwl new file mode 100644 index 0000000..3474e71 --- /dev/null +++ b/variant_annotation/chipvar_processing.cwl @@ -0,0 +1,60 @@ +class: Workflow +cwlVersion: v1.0 +id: chipvar_processing +label: chipvar_processing +$namespaces: + sbg: 'https://www.sevenbridges.com/' +inputs: + - id: input_variant_annotated_maf + type: File + 'sbg:x': -533 + 'sbg:y': -122.5 + - id: output_maf_name_filter + type: string? + 'sbg:x': -453 + 'sbg:y': -272.5 + - id: output_maf_name_tag + type: string? + 'sbg:x': -139 + 'sbg:y': -247.5 +outputs: + - id: output_maf_cmoch_filtered + outputSource: + - pv_maf_filter/output + type: File? + 'sbg:x': -183 + 'sbg:y': 111 + - id: output_maf_cmoch_tag + outputSource: + - pv_maf_tag/output + type: File? + 'sbg:x': 175 + 'sbg:y': 74.5 +steps: + - id: pv_maf_filter + in: + - id: input_maf + source: input_variant_annotated_maf + - id: output_maf_name + source: output_maf_name_filter + out: + - id: output + run: >- + ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_filter_cmoch/maf_filter_cmoch.cwl + label: pv_maf_filter + 'sbg:x': -369 + 'sbg:y': -112.5 + - id: pv_maf_tag + in: + - id: input_maf + source: pv_maf_filter/output + - id: output_maf_name + source: output_maf_name_tag + out: + - id: output + run: >- + ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_tag_cmoch/maf_tag_cmoch.cwl + label: pv_maf_tag + 'sbg:x': -40 + 'sbg:y': -109.5 +requirements: [] diff --git a/variant_annotation/example_inputs_chipvar.yaml b/variant_annotation/example_inputs_chipvar.yaml new file mode 100644 index 0000000..8c81fd9 --- /dev/null +++ b/variant_annotation/example_inputs_chipvar.yaml @@ -0,0 +1,5 @@ +input_variant_annotated_maf: + class: File + path: /path/tovariant/annotated/maf +output_maf_name_filter: annotated_cmoch_filter.maf +output_maf_name_tag: annotated_cmoch-tag.maf diff --git a/variant_annotation/example_inputs.yaml b/variant_annotation/example_inputs_variant_annotation.yaml similarity index 100% rename from variant_annotation/example_inputs.yaml rename to variant_annotation/example_inputs_variant_annotation.yaml From 8a8ae234eef0f779bbd0777d0564b29b1e3aa658 Mon Sep 17 00:00:00 2001 From: Karthigayini Sivaprakasam Date: Wed, 27 Dec 2023 15:45:26 -0600 Subject: [PATCH 06/19] updated Readme --- variant_annotation/README.md | 69 ++++++++++++++++++++++++++++++------ 1 file changed, 59 insertions(+), 10 deletions(-) diff --git a/variant_annotation/README.md b/variant_annotation/README.md index 57702e3..0fb3486 100644 --- a/variant_annotation/README.md +++ b/variant_annotation/README.md @@ -6,27 +6,39 @@ - [snpift](https://msk-access.gitbook.io/command-line-tools-cwl/snpsift_annotate_5.0/) - [vcf2maf](https://msk-access.gitbook.io/command-line-tools-cwl/vcf2maf_1.6.21/) -- [maf_annotated_by_bed](https://msk-access.gitbook.io/command-line-tools-cwl/postprocessing_variant_calls/0.2.0/maf_annotated_by_bed/) +- [maf_annotated_by_bed](https://msk-access.gitbook.io/command-line-tools-cwl/postprocessing_variant_calls/0.2.3/maf_annotated_by_bed/) +- [maf_annotated_by_tsv](https://msk-access.gitbook.io/command-line-tools-cwl/postprocessing_variant_calls/0.2.3/maf_annotated_by_tsv/) #### Usage ```bash usage: variant_annotation.cwl - [-h] --input_cosmicCountDB_vcf INPUT_COSMICCOUNTDB_VCF + [-h] --input_cosmicCountDB_vcf INPUT_COSMICCOUNTDB_VCF --vardict_input_vcf VARDICT_INPUT_VCF --input_cosmicprevalenceDB_vcf INPUT_COSMICPREVALENCEDB_VCF [--min_hom_vaf MIN_HOM_VAF] [--output_vcf2mafName OUTPUT_VCF2MAFNAME] [--retain_info RETAIN_INFO] [--tumor_id TUMOR_ID] [--snpsift_countOpName SNPSIFT_COUNTOPNAME] [--snpsift_prevalOpName SNPSIFT_PREVALOPNAME] --opOncoKbMafName OPONCOKBMAFNAME --oncoKbApiToken ONCOKBAPITOKEN - [--oncoKbAnnotateHotspots] --input_complexity_bed INPUT_COMPLEXITY_BED - --input_DUST_bed INPUT_DUST_BED - [--output_DUST_filename OUTPUT_DUST_FILENAME] - [--column_name_DUST COLUMN_NAME_DUST] - [--output_complexity_filename OUTPUT_COMPLEXITY_FILENAME] + [--oncoKbAnnotateHotspots] --input_mappability_bed + INPUT_MAPPABILITY_BED --input_complexity_bed INPUT_COMPLEXITY_BED + --output_mappability_filename OUTPUT_MAPPABILITY_FILENAME + [--column_name_mappability COLUMN_NAME_MAPPABILITY] + --output_complexity_filename OUTPUT_COMPLEXITY_FILENAME [--column_name_complexity COLUMN_NAME_COMPLEXITY] + --input_hotspot_tsv_file INPUT_HOTSPOT_TSV_FILE + [--output_column_name_hotpsot OUTPUT_COLUMN_NAME_HOTPSOT] + [--output_hotspot_maf_name OUTPUT_HOTSPOT_MAF_NAME] + --input_47kchpd_tsv_file INPUT_47KCHPD_TSV_FILE + [--output_47kchpd_maf_name OUTPUT_47KCHPD_MAF_NAME] + [--output_column_name_47kchpd OUTPUT_COLUMN_NAME_47KCHPD] + --input_panmeloid_tsv_file INPUT_PANMELOID_TSV_FILE + [--output_maf_name_panmyeloid OUTPUT_MAF_NAME_PANMYELOID] + [--output_column_name_panmyeloid OUTPUT_COLUMN_NAME_PANMYELOID] [job_order] +variant_annotation + positional arguments: job_order Job input json file @@ -44,11 +56,48 @@ optional arguments: --opOncoKbMafName OPONCOKBMAFNAME --oncoKbApiToken ONCOKBAPITOKEN --oncoKbAnnotateHotspots + --input_mappability_bed INPUT_MAPPABILITY_BED --input_complexity_bed INPUT_COMPLEXITY_BED - --input_DUST_bed INPUT_DUST_BED - --output_DUST_filename OUTPUT_DUST_FILENAME - --column_name_DUST COLUMN_NAME_DUST + --output_mappability_filename OUTPUT_MAPPABILITY_FILENAME + --column_name_mappability COLUMN_NAME_MAPPABILITY --output_complexity_filename OUTPUT_COMPLEXITY_FILENAME --column_name_complexity COLUMN_NAME_COMPLEXITY + --input_hotspot_tsv_file INPUT_HOTSPOT_TSV_FILE + --output_column_name_hotpsot OUTPUT_COLUMN_NAME_HOTPSOT + --output_hotspot_maf_name OUTPUT_HOTSPOT_MAF_NAME + --input_47kchpd_tsv_file INPUT_47KCHPD_TSV_FILE + --output_47kchpd_maf_name OUTPUT_47KCHPD_MAF_NAME + --output_column_name_47kchpd OUTPUT_COLUMN_NAME_47KCHPD + --input_panmeloid_tsv_file INPUT_PANMELOID_TSV_FILE + --output_maf_name_panmyeloid OUTPUT_MAF_NAME_PANMYELOID + --output_column_name_panmyeloid OUTPUT_COLUMN_NAME_PANMYELOID +``` + +## Chipvar_postprocessing + +### Tools used + +- [maf_filter_cmoch](https://msk-access.gitbook.io/command-line-tools-cwl/postprocessing_variant_calls/0.2.3/maf_filter_cmoch/) +- [maf_tag_cmoch](https://msk-access.gitbook.io/command-line-tools-cwl/postprocessing_variant_calls/0.2.3/maf_tag_cmoch/) + +#### Usage + +``` +usage: chipvar_processing.cwl +[-h] --input_variant_annotated_maf INPUT_VARIANT_ANNOTATED_MAF + [--output_maf_name_filter OUTPUT_MAF_NAME_FILTER] + [--output_maf_name_tag OUTPUT_MAF_NAME_TAG] + [job_order] + +chipvar_processing + +positional arguments: + job_order Job input json file + +optional arguments: + -h, --help show this help message and exit + --input_variant_annotated_maf INPUT_VARIANT_ANNOTATED_MAF + --output_maf_name_filter OUTPUT_MAF_NAME_FILTER + --output_maf_name_tag OUTPUT_MAF_NAME_TAG ``` From c0217413c7386178e7e808d8d3c53bd40cbf8b3f Mon Sep 17 00:00:00 2001 From: Karthigayini Sivaprakasam Date: Fri, 29 Dec 2023 12:49:02 -0600 Subject: [PATCH 07/19] extra output --- variant_annotation/variant_annotation.cwl | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/variant_annotation/variant_annotation.cwl b/variant_annotation/variant_annotation.cwl index 246d1ed..5e85298 100755 --- a/variant_annotation/variant_annotation.cwl +++ b/variant_annotation/variant_annotation.cwl @@ -155,12 +155,6 @@ outputs: type: File 'sbg:x': 2283.204345703125 'sbg:y': 275.9561767578125 - - id: output - outputSource: - - maf_annotated_by_bed_1/output - type: File - 'sbg:x': 2380.1826171875 - 'sbg:y': 616.3430786132812 - id: output_hotspot_maf outputSource: - pv_maf_annotated_by_tsv/output @@ -298,7 +292,7 @@ steps: out: - id: output run: >- - ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_annotate_by_tsv/maf_annotate_by_tsv.cwl + ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_annotated_by_tsv/maf_annotated_by_tsv.cwl label: pv_maf_annotatedByTsv 'sbg:x': 2624.56201171875 'sbg:y': 446.36090087890625 @@ -315,7 +309,7 @@ steps: out: - id: output run: >- - ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_annotate_by_tsv/maf_annotate_by_tsv.cwl + ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_annotated_by_tsv/maf_annotated_by_tsv.cwl label: pv_maf_annotatedByTsv 'sbg:x': 3027.093994140625 'sbg:y': 444.81915283203125 @@ -332,7 +326,7 @@ steps: out: - id: output run: >- - ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_annotate_by_tsv/maf_annotate_by_tsv.cwl + ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_annotated_by_tsv/maf_annotated_by_tsv.cwl label: pv_maf_annotatedByTsv 'sbg:x': 3366.108154296875 'sbg:y': 434.5843505859375 From fb016a0569da682b8fec4ec664e52a804a128262 Mon Sep 17 00:00:00 2001 From: Karthigayini Sivaprakasam Date: Tue, 2 Jan 2024 11:49:32 -0600 Subject: [PATCH 08/19] Update chipvar_processing.cwl --- variant_annotation/chipvar_processing.cwl | 28 +++++++++++------------ 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/variant_annotation/chipvar_processing.cwl b/variant_annotation/chipvar_processing.cwl index 3474e71..2b38c67 100644 --- a/variant_annotation/chipvar_processing.cwl +++ b/variant_annotation/chipvar_processing.cwl @@ -5,18 +5,18 @@ label: chipvar_processing $namespaces: sbg: 'https://www.sevenbridges.com/' inputs: - - id: input_variant_annotated_maf - type: File - 'sbg:x': -533 - 'sbg:y': -122.5 - id: output_maf_name_filter type: string? 'sbg:x': -453 'sbg:y': -272.5 - id: output_maf_name_tag type: string? - 'sbg:x': -139 - 'sbg:y': -247.5 + 'sbg:x': -911 + 'sbg:y': -200 + - id: input_variant_annotated_maf + type: File + 'sbg:x': -1012.5234375 + 'sbg:y': 20 outputs: - id: output_maf_cmoch_filtered outputSource: @@ -28,13 +28,13 @@ outputs: outputSource: - pv_maf_tag/output type: File? - 'sbg:x': 175 - 'sbg:y': 74.5 + 'sbg:x': -559 + 'sbg:y': 104 steps: - id: pv_maf_filter in: - id: input_maf - source: input_variant_annotated_maf + source: pv_maf_tag/output - id: output_maf_name source: output_maf_name_filter out: @@ -42,12 +42,12 @@ steps: run: >- ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_filter_cmoch/maf_filter_cmoch.cwl label: pv_maf_filter - 'sbg:x': -369 - 'sbg:y': -112.5 + 'sbg:x': -303 + 'sbg:y': -116 - id: pv_maf_tag in: - id: input_maf - source: pv_maf_filter/output + source: input_variant_annotated_maf - id: output_maf_name source: output_maf_name_tag out: @@ -55,6 +55,6 @@ steps: run: >- ../command_line_tools/postprocessing_variant_calls/0.2.3/maf_tag_cmoch/maf_tag_cmoch.cwl label: pv_maf_tag - 'sbg:x': -40 - 'sbg:y': -109.5 + 'sbg:x': -777 + 'sbg:y': -80 requirements: [] From 31cb56e1abc6c82c035a9c49a00bfa073c178401 Mon Sep 17 00:00:00 2001 From: Karthigayini Sivaprakasam Date: Wed, 3 Jan 2024 10:50:54 -0600 Subject: [PATCH 09/19] updating cmdlinetools --- command_line_tools | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/command_line_tools b/command_line_tools index 658de77..cc58685 160000 --- a/command_line_tools +++ b/command_line_tools @@ -1 +1 @@ -Subproject commit 658de774e792d65668de9becb7e8a18775723534 +Subproject commit cc58685fe56190aa48a1213af41952039fddc6b8 From 743246bbcd3c902f4eadf3458b49b1422bda2cde Mon Sep 17 00:00:00 2001 From: Karthigayini Sivaprakasam Date: Wed, 3 Jan 2024 18:41:32 +0000 Subject: [PATCH 10/19] Commit from GitHub Actions --- .../chipvar_processing__packed.cwl | 380 ++++++++++++ .../variant_annotation__packed.cwl | 564 +++++++++++++++--- 2 files changed, 850 insertions(+), 94 deletions(-) create mode 100644 variant_annotation/chipvar_processing__packed.cwl diff --git a/variant_annotation/chipvar_processing__packed.cwl b/variant_annotation/chipvar_processing__packed.cwl new file mode 100644 index 0000000..993f1fc --- /dev/null +++ b/variant_annotation/chipvar_processing__packed.cwl @@ -0,0 +1,380 @@ +{ + "$graph": [ + { + "class": "CommandLineTool", + "id": "#maf_filter_cmoch.cwl", + "baseCommand": [ + "pv" + ], + "inputs": [ + { + "id": "#maf_filter_cmoch.cwl/pv_maf_filter/memory_per_job", + "type": [ + "null", + "int" + ], + "doc": "Memory per job in megabytes" + }, + { + "id": "#maf_filter_cmoch.cwl/pv_maf_filter/memory_overhead", + "type": [ + "null", + "int" + ], + "doc": "Memory overhead per job in megabytes" + }, + { + "id": "#maf_filter_cmoch.cwl/pv_maf_filter/number_of_threads", + "type": [ + "null", + "int" + ] + }, + { + "id": "#maf_filter_cmoch.cwl/pv_maf_filter/input_maf", + "type": "File", + "inputBinding": { + "position": 0, + "prefix": "-m" + } + }, + { + "id": "#maf_filter_cmoch.cwl/pv_maf_filter/output_maf_name", + "type": [ + "null", + "string" + ], + "inputBinding": { + "position": 0, + "prefix": "-o" + }, + "https://www.sevenbridges.com/toolDefaultValue": "output.maf" + }, + { + "id": "#maf_filter_cmoch.cwl/pv_maf_filter/output_maf_separator", + "type": [ + "null", + "string" + ], + "inputBinding": { + "position": 0, + "prefix": "-sep" + }, + "https://www.sevenbridges.com/toolDefaultValue": "tsv" + } + ], + "label": "pv_maf_filter", + "arguments": [ + "maf", + "filter", + "cmo_ch", + { + "position": 2, + "prefix": "--output", + "valueFrom": "${ \n if (inputs.output_maf_name) { \n return inputs.output_maf_name \n } else { \n return inputs.input_maf.basename.replace('.maf', '_maftagcmoCh.maf') \n } \n}" + } + ], + "requirements": [ + { + "class": "ResourceRequirement", + "ramMin": 8000, + "coresMin": 2 + }, + { + "class": "DockerRequirement", + "dockerPull": 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"type": "string", + "type": [ + "null", + "string" + ], "inputBinding": { "position": 0, "prefix": "-o" @@ -96,6 +99,13 @@ } ], "label": "oncokb_annotator", + "arguments": [ + { + "position": 0, + "prefix": "-o", + "valueFrom": "${\n if(inputs.outputMafName){\n return inputs.outputMafName\n } else {\n return inputs.inputMafFile.basename.replace('.maf', '_oncoKB.maf')\n }\n}" + } + ], "requirements": [ { "class": "DockerRequirement", @@ -147,7 +157,7 @@ "File" ], "outputBinding": { - "glob": "$(inputs.outputMafName)" + "glob": "${ \n if (inputs.outputMafName) { \n return inputs.outputMafName\n } else { \n return inputs.inputMafFile.basename.replace('.maf', '_oncoKB.maf') \n } \n}" } } ] @@ -200,10 +210,7 @@ }, { "id": "#maf_annotated_by_bed.cwl/maf_annotated_by_bed/output_filename", - "type": [ - "null", - "string" - ], + "type": "string", "inputBinding": { "position": 3, "prefix": "-o" @@ -227,7 +234,7 @@ "id": "#maf_annotated_by_bed.cwl/maf_annotated_by_bed/output", "type": "File", 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2759.510498046875, + "https://www.sevenbridges.com/y": 265.0616149902344 + }, + { + "id": "#main/output_47kchpd_maf_name", + "type": [ + "null", + "string" + ], + "https://www.sevenbridges.com/x": 3004.045654296875, + "https://www.sevenbridges.com/y": 208.01800537109375 + }, + { + "id": "#main/output_column_name_47kchpd", + "type": [ + "null", + "string" + ], + "https://www.sevenbridges.com/x": 2837.483642578125, + "https://www.sevenbridges.com/y": 590.1929931640625 + }, + { + "id": "#main/input_panmeloid_tsv_file", + "type": "File", + "https://www.sevenbridges.com/x": 3165.773193359375, + "https://www.sevenbridges.com/y": 219.0523681640625 + }, + { + "id": "#main/output_maf_name_panmyeloid", + "type": [ + "null", + "string" + ], + "https://www.sevenbridges.com/x": 3330.037841796875, + "https://www.sevenbridges.com/y": 199.72714233398438 + }, + { + "id": "#main/output_column_name_panmyeloid", + "type": [ + "null", + "string" + ], + "https://www.sevenbridges.com/x": 3216.4921875, + "https://www.sevenbridges.com/y": 559.9721069335938 } ], "outputs": [ @@ -979,8 +1229,8 @@ "#main/snpsift_annotate_5_0/annotatedOutput" ], "type": "File", - "https://www.sevenbridges.com/x": 348.4152526855469, - "https://www.sevenbridges.com/y": 772.9266967773438 + "https://www.sevenbridges.com/x": 224.51815795898438, + "https://www.sevenbridges.com/y": 602.496337890625 }, { "id": "#main/annotatedOutput_prevalence", @@ -988,8 +1238,8 @@ "#main/snpsift_annotate_5_1/annotatedOutput" ], "type": "File", - "https://www.sevenbridges.com/x": 656.337158203125, - "https://www.sevenbridges.com/y": 723.7005615234375 + "https://www.sevenbridges.com/x": 714.343017578125, + "https://www.sevenbridges.com/y": 463.94891357421875 }, { "id": "#main/vcf2maf_maf", @@ -997,38 +1247,74 @@ "#main/vcf2maf_v1_6_21/vcf2maf_maf" ], "type": "File", - "https://www.sevenbridges.com/x": 1148.8089599609375, - "https://www.sevenbridges.com/y": 594.5475463867188 + "https://www.sevenbridges.com/x": 1163.603759765625, + "https://www.sevenbridges.com/y": 246.265625 + }, + { + "id": "#main/oncokb_maf", + "outputSource": [ + "#main/oncokb_annotator/outputMaf" + ], + "type": [ + "null", + "File" + ], + "https://www.sevenbridges.com/x": 1504.72998046875, + "https://www.sevenbridges.com/y": 733.0220336914062 }, { - "id": "#main/output_mappability_maf", + "id": "#main/output_mapability_maf", "outputSource": [ - "#main/maf_annotated_by_bed_mappability/output" + "#main/maf_annotated_by_bed/output" ], "type": "File", - "https://www.sevenbridges.com/x": 1524.598876953125, - "https://www.sevenbridges.com/y": 679.8934936523438 + "https://www.sevenbridges.com/x": 2008.9051513671875, + "https://www.sevenbridges.com/y": 272.00726318359375 }, { "id": "#main/output_complexity_maf", "outputSource": [ - "#main/maf_annotated_by_bed_lowComplexity/output" + "#main/maf_annotated_by_bed_1/output" ], "type": "File", - "https://www.sevenbridges.com/x": 1815.8809814453125, - "https://www.sevenbridges.com/y": 248.1118621826172 + "https://www.sevenbridges.com/x": 2283.204345703125, + "https://www.sevenbridges.com/y": 275.9561767578125 }, { - "id": "#main/oncokb_maf", + "id": "#main/output_hotspot_maf", "outputSource": [ - "#main/oncokb_annotator/outputMaf" + "#main/pv_maf_annotated_by_tsv/output" + ], + "type": [ + "null", + "File" + ], + "https://www.sevenbridges.com/x": 2793.349609375, + "https://www.sevenbridges.com/y": 755.3427734375 + }, + { + "id": "#main/output_47kchpd_maf", + "outputSource": [ + "#main/pv_maf_annotated_by_tsv_1/output" + ], + "type": [ + "null", + "File" + ], + "https://www.sevenbridges.com/x": 3171.963623046875, + "https://www.sevenbridges.com/y": 695.1704711914062 + }, + { + "id": "#main/output_panmyeloid_maf", + "outputSource": [ + "#main/pv_maf_annotated_by_tsv_2/output" ], "type": [ "null", "File" ], - "https://www.sevenbridges.com/x": 1327.9454345703125, - "https://www.sevenbridges.com/y": 738.3821411132812 + "https://www.sevenbridges.com/x": 3498.328369140625, + "https://www.sevenbridges.com/y": 604.7518310546875 } ], "steps": [ @@ -1055,8 +1341,8 @@ ], "run": "#snpsift_annotate_5-0.cwl", "label": "snpsift_countAnnotation", - "https://www.sevenbridges.com/x": 155.640625, - "https://www.sevenbridges.com/y": 320.390625 + "https://www.sevenbridges.com/x": 245.35765075683594, + "https://www.sevenbridges.com/y": 251.2992401123047 }, { "id": "#main/snpsift_annotate_5_1", @@ -1081,8 +1367,8 @@ ], "run": "#snpsift_annotate_5-0.cwl", "label": "snpsift_annotate_5.0", - "https://www.sevenbridges.com/x": 416.7921447753906, - "https://www.sevenbridges.com/y": 113.796875 + "https://www.sevenbridges.com/x": 639.072998046875, + "https://www.sevenbridges.com/y": 278.7226257324219 }, { "id": "#main/vcf2maf_v1_6_21", @@ -1130,8 +1416,8 @@ } ], "run": "#vcf2maf_1.6.21.cwl", - "https://www.sevenbridges.com/x": 833.5098266601562, - "https://www.sevenbridges.com/y": 276.9501953125 + "https://www.sevenbridges.com/x": 1015.934326171875, + "https://www.sevenbridges.com/y": 356.05108642578125 }, { "id": "#main/oncokb_annotator", @@ -1164,68 +1450,158 @@ ], "run": "#oncokb_annotator_3-2-2.cwl", "label": "oncokb_annotator", - "https://www.sevenbridges.com/x": 1096.5919189453125, - "https://www.sevenbridges.com/y": 261 + "https://www.sevenbridges.com/x": 1426.226318359375, + "https://www.sevenbridges.com/y": 402.77374267578125 }, { - "id": "#main/maf_annotated_by_bed_mappability", + "id": "#main/maf_annotated_by_bed", "in": [ { - "id": "#main/maf_annotated_by_bed_mappability/input_maf", + "id": "#main/maf_annotated_by_bed/input_maf", "source": "#main/oncokb_annotator/outputMaf" }, { - "id": "#main/maf_annotated_by_bed_mappability/input_bed", + "id": "#main/maf_annotated_by_bed/input_bed", "source": "#main/input_mappability_bed" }, { - "id": "#main/maf_annotated_by_bed_mappability/output_filename", + "id": "#main/maf_annotated_by_bed/output_filename", "source": "#main/output_mappability_filename" }, { - "id": "#main/maf_annotated_by_bed_mappability/column_name", + "id": "#main/maf_annotated_by_bed/column_name", "source": "#main/column_name_mappability" } ], "out": [ { - "id": "#main/maf_annotated_by_bed_mappability/output" + "id": "#main/maf_annotated_by_bed/output" } ], "run": "#maf_annotated_by_bed.cwl", "label": "maf_annotated_by_bed", - "https://www.sevenbridges.com/x": 1317.3984375, - "https://www.sevenbridges.com/y": 267 + "https://www.sevenbridges.com/x": 1838.0584716796875, + "https://www.sevenbridges.com/y": 425.2846984863281 }, { - "id": "#main/maf_annotated_by_bed_lowComplexity", + "id": "#main/maf_annotated_by_bed_1", "in": [ { - "id": "#main/maf_annotated_by_bed_lowComplexity/input_maf", - "source": "#main/maf_annotated_by_bed_mappability/output" + "id": "#main/maf_annotated_by_bed_1/input_maf", + "source": "#main/maf_annotated_by_bed/output" }, { - "id": "#main/maf_annotated_by_bed_lowComplexity/input_bed", + "id": "#main/maf_annotated_by_bed_1/input_bed", "source": "#main/input_complexity_bed" }, { - "id": "#main/maf_annotated_by_bed_lowComplexity/output_filename", + "id": "#main/maf_annotated_by_bed_1/output_filename", "source": "#main/output_complexity_filename" }, { - "id": "#main/maf_annotated_by_bed_lowComplexity/column_name", + "id": "#main/maf_annotated_by_bed_1/column_name", "source": "#main/column_name_complexity" } ], "out": [ { - "id": "#main/maf_annotated_by_bed_lowComplexity/output" + "id": "#main/maf_annotated_by_bed_1/output" } ], "run": "#maf_annotated_by_bed.cwl", "label": "maf_annotated_by_bed", - "https://www.sevenbridges.com/x": 1600, - "https://www.sevenbridges.com/y": 262.8888854980469 + "https://www.sevenbridges.com/x": 2220.102294921875, + "https://www.sevenbridges.com/y": 478.15325927734375 + }, + { + "id": "#main/pv_maf_annotated_by_tsv", + "in": [ + { + "id": "#main/pv_maf_annotated_by_tsv/input_maf", + "source": "#main/maf_annotated_by_bed_1/output" + }, + { + "id": "#main/pv_maf_annotated_by_tsv/output_maf_name", + "source": "#main/output_hotspot_maf_name" + }, + { + "id": "#main/pv_maf_annotated_by_tsv/output_column_name", + "source": "#main/output_column_name_hotpsot" + }, + { + "id": "#main/pv_maf_annotated_by_tsv/input_tsv_file", + "source": "#main/input_hotspot_tsv_file" + } + ], + "out": [ + { + "id": "#main/pv_maf_annotated_by_tsv/output" + } + ], + "run": "#maf_annotated_by_tsv.cwl", + "label": "pv_maf_annotatedByTsv", + "https://www.sevenbridges.com/x": 2624.56201171875, + "https://www.sevenbridges.com/y": 446.36090087890625 + }, + { + "id": "#main/pv_maf_annotated_by_tsv_1", + "in": [ + { + "id": "#main/pv_maf_annotated_by_tsv_1/input_maf", + "source": "#main/pv_maf_annotated_by_tsv/output" + }, + { + "id": "#main/pv_maf_annotated_by_tsv_1/output_maf_name", + "source": "#main/output_47kchpd_maf_name" + }, + { + "id": "#main/pv_maf_annotated_by_tsv_1/output_column_name", + "source": "#main/output_column_name_47kchpd" + }, + { + "id": "#main/pv_maf_annotated_by_tsv_1/input_tsv_file", + "source": "#main/input_47kchpd_tsv_file" + } + ], + "out": [ + { + "id": "#main/pv_maf_annotated_by_tsv_1/output" + } + ], + "run": "#maf_annotated_by_tsv.cwl", + "label": "pv_maf_annotatedByTsv", + "https://www.sevenbridges.com/x": 3027.093994140625, + "https://www.sevenbridges.com/y": 444.81915283203125 + }, + { + "id": "#main/pv_maf_annotated_by_tsv_2", + "in": [ + { + "id": "#main/pv_maf_annotated_by_tsv_2/input_maf", + "source": "#main/pv_maf_annotated_by_tsv_1/output" + }, + { + "id": "#main/pv_maf_annotated_by_tsv_2/output_maf_name", + "source": "#main/output_maf_name_panmyeloid" + }, + { + "id": "#main/pv_maf_annotated_by_tsv_2/output_column_name", + "source": "#main/output_column_name_panmyeloid" + }, + { + "id": "#main/pv_maf_annotated_by_tsv_2/input_tsv_file", + "source": "#main/input_panmeloid_tsv_file" + } + ], + "out": [ + { + "id": "#main/pv_maf_annotated_by_tsv_2/output" + } + ], + "run": "#maf_annotated_by_tsv.cwl", + "label": "pv_maf_annotatedByTsv", + "https://www.sevenbridges.com/x": 3366.108154296875, + "https://www.sevenbridges.com/y": 434.5843505859375 } ], "requirements": [], From 0c2b2593b613114cbafd3b216702672b0d823ad0 Mon Sep 17 00:00:00 2001 From: Karthigayini Sivaprakasam Date: Wed, 10 Jan 2024 14:25:49 -0600 Subject: [PATCH 11/19] Update command_line_tools --- command_line_tools | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/command_line_tools b/command_line_tools index cc58685..3eca25c 160000 --- a/command_line_tools +++ b/command_line_tools @@ -1 +1 @@ -Subproject commit cc58685fe56190aa48a1213af41952039fddc6b8 +Subproject commit 3eca25c94639db6f7347d4e60d0d2a5654d297c8 From d554862eb9f0c9decf39a6dbb35554414129c84d Mon Sep 17 00:00:00 2001 From: Karthigayini Sivaprakasam Date: Wed, 10 Jan 2024 20:35:55 +0000 Subject: [PATCH 12/19] Commit from GitHub Actions --- variant_annotation/chipvar_processing__packed.cwl | 4 ++-- variant_annotation/variant_annotation__packed.cwl | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/variant_annotation/chipvar_processing__packed.cwl b/variant_annotation/chipvar_processing__packed.cwl index 993f1fc..7139180 100644 --- a/variant_annotation/chipvar_processing__packed.cwl +++ b/variant_annotation/chipvar_processing__packed.cwl @@ -82,7 +82,7 @@ }, { "class": "DockerRequirement", - "dockerPull": "ghcr.io/msk-access/postprocessing_variant_calls:chipvar_dev10" + "dockerPull": "ghcr.io/msk-access/postprocessing_variant_calls:0.2.3" }, { "class": "InlineJavascriptRequirement" @@ -228,7 +228,7 @@ }, { "class": "DockerRequirement", - "dockerPull": "ghcr.io/msk-access/postprocessing_variant_calls:chipvar_dev10" + "dockerPull": "ghcr.io/msk-access/postprocessing_variant_calls:0.2.3" }, { "class": "InlineJavascriptRequirement" diff --git a/variant_annotation/variant_annotation__packed.cwl b/variant_annotation/variant_annotation__packed.cwl index 2842922..96ea670 100644 --- a/variant_annotation/variant_annotation__packed.cwl +++ b/variant_annotation/variant_annotation__packed.cwl @@ -257,7 +257,7 @@ }, { "class": "DockerRequirement", - "dockerPull": "ghcr.io/msk-access/postprocessing_variant_calls:chipvar_dev10" + "dockerPull": "ghcr.io/msk-access/postprocessing_variant_calls:0.2.3" }, { "class": "InlineJavascriptRequirement" @@ -424,7 +424,7 @@ }, { "class": "DockerRequirement", - "dockerPull": "ghcr.io/msk-access/postprocessing_variant_calls:chipvar_dev10" + "dockerPull": "ghcr.io/msk-access/postprocessing_variant_calls:0.2.3" }, { "class": "InlineJavascriptRequirement" From 8d7515e853b671fc5fd889f6ac2e7ef1f349371b Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Mon, 17 Jun 2024 23:21:44 -0400 Subject: [PATCH 13/19] Adding 0.2.15 version of biometrics --- command_line_tools | 2 +- qc_collapsed_bam/qc_collapsed_bam_v2.0.cwl | 26 +++++++++++----------- qc_duplex_bam/qc_duplex_bam_v2.0.cwl | 20 ++++++++--------- 3 files changed, 24 insertions(+), 24 deletions(-) diff --git a/command_line_tools b/command_line_tools index 3eca25c..d61c917 160000 --- a/command_line_tools +++ b/command_line_tools @@ -1 +1 @@ -Subproject commit 3eca25c94639db6f7347d4e60d0d2a5654d297c8 +Subproject commit d61c9170bf84b35368eadfb3a522c6d143b93b55 diff --git a/qc_collapsed_bam/qc_collapsed_bam_v2.0.cwl b/qc_collapsed_bam/qc_collapsed_bam_v2.0.cwl index 3040723..7110473 100755 --- a/qc_collapsed_bam/qc_collapsed_bam_v2.0.cwl +++ b/qc_collapsed_bam/qc_collapsed_bam_v2.0.cwl @@ -317,25 +317,25 @@ outputs: 'sbg:y': 884.875 - id: biometrics_major_plot outputSource: - - biometrics_major_0_2_14/biometrics_major_plot + - biometrics_major_0_2_15/biometrics_major_plot type: File? 'sbg:x': 1482.3623046875 'sbg:y': 1496.25 - id: biometrics_major_json outputSource: - - biometrics_major_0_2_14/biometrics_major_json + - biometrics_major_0_2_15/biometrics_major_json type: File? 'sbg:x': 1482.3623046875 'sbg:y': 1603.125 - id: biometrics_major_csv outputSource: - - biometrics_major_0_2_14/biometrics_major_csv + - biometrics_major_0_2_15/biometrics_major_csv type: File 'sbg:x': 1482.3623046875 'sbg:y': 1710 - id: collapsed_biometrics_extract_pickle outputSource: - - biometrics_extract_0_2_14/biometrics_extract_pickle + - biometrics_extract_0_2_15/biometrics_extract_pickle type: File 'sbg:x': 982.1435546875 'sbg:y': 2214.5 @@ -397,7 +397,7 @@ steps: - id: input linkMerge: merge_nested source: - - biometrics_extract_0_2_14/biometrics_extract_pickle + - biometrics_extract_0_2_15/biometrics_extract_pickle - id: minor_threshold source: minor_threshold - id: prefix @@ -414,7 +414,7 @@ steps: - id: biometrics_minor_json - id: biometrics_minor_plot - id: biometrics_minor_sites_plot - run: ../command_line_tools/biometrics_minor/0.2.14/biometrics_minor.cwl + run: ../command_line_tools/biometrics_minor/0.2.15/biometrics_minor.cwl 'sbg:x': 982.1435546875 'sbg:y': 1916.75 - id: biometrics_sexmismatch @@ -422,7 +422,7 @@ steps: - id: input linkMerge: merge_flattened source: - - biometrics_extract_0_2_14/biometrics_extract_pickle + - biometrics_extract_0_2_15/biometrics_extract_pickle - id: coverage_threshold source: coverage_threshold - id: prefix @@ -435,15 +435,15 @@ steps: - id: biometrics_sexmismatch_csv - id: biometrics_sexmismatch_json run: >- - ../command_line_tools/biometrics_sexmismatch/0.2.14/biometrics_sexmismatch.cwl + ../command_line_tools/biometrics_sexmismatch/0.2.15/biometrics_sexmismatch.cwl 'sbg:x': 982.1435546875 'sbg:y': 1760.875 - - id: biometrics_major_0_2_14 + - id: biometrics_major_0_2_15 in: - id: input linkMerge: merge_nested source: - - biometrics_extract_0_2_14/biometrics_extract_pickle + - biometrics_extract_0_2_15/biometrics_extract_pickle - id: major_threshold source: major_threshold - id: prefix @@ -458,10 +458,10 @@ steps: - id: biometrics_major_csv - id: biometrics_major_json - id: biometrics_major_plot - run: ../command_line_tools/biometrics_major/0.2.14/biometrics_major.cwl + run: ../command_line_tools/biometrics_major/0.2.15/biometrics_major.cwl 'sbg:x': 982.1435546875 'sbg:y': 2079.625 - - id: biometrics_extract_0_2_14 + - id: biometrics_extract_0_2_15 in: - id: sample_bam source: collapsed_bam @@ -482,7 +482,7 @@ steps: source: collapsed_biometrics_extract_file_type out: - id: biometrics_extract_pickle - run: ../command_line_tools/biometrics_extract/0.2.14/biometrics_extract.cwl + run: ../command_line_tools/biometrics_extract/0.2.15/biometrics_extract.cwl 'sbg:x': 351.4375 'sbg:y': 1328.9375 - id: getbasecountsmultisample_1_2_5 diff --git a/qc_duplex_bam/qc_duplex_bam_v2.0.cwl b/qc_duplex_bam/qc_duplex_bam_v2.0.cwl index d720bcf..1ff6c2b 100755 --- a/qc_duplex_bam/qc_duplex_bam_v2.0.cwl +++ b/qc_duplex_bam/qc_duplex_bam_v2.0.cwl @@ -268,31 +268,31 @@ outputs: 'sbg:y': 750.8828125 - id: duplex_biometrics_extract_pickle outputSource: - - biometrics_extract_0_2_14/biometrics_extract_pickle + - biometrics_extract_0_2_15/biometrics_extract_pickle type: File 'sbg:x': 984.2216796875 'sbg:y': 2556.359375 - id: biometrics_minor_sites_plot outputSource: - - biometrics_minor_0_2_14/biometrics_minor_sites_plot + - biometrics_minor_0_2_15/biometrics_minor_sites_plot type: File? 'sbg:x': 1432.8466796875 'sbg:y': 1120.1640625 - id: biometrics_minor_plot outputSource: - - biometrics_minor_0_2_14/biometrics_minor_plot + - biometrics_minor_0_2_15/biometrics_minor_plot type: File? 'sbg:x': 1432.8466796875 'sbg:y': 1226.8203125 - id: biometrics_minor_json outputSource: - - biometrics_minor_0_2_14/biometrics_minor_json + - biometrics_minor_0_2_15/biometrics_minor_json type: File? 'sbg:x': 1432.8466796875 'sbg:y': 1333.515625 - id: biometrics_minor_csv outputSource: - - biometrics_minor_0_2_14/biometrics_minor_csv + - biometrics_minor_0_2_15/biometrics_minor_csv type: File 'sbg:x': 1432.8466796875 'sbg:y': 1440.2109375 @@ -384,7 +384,7 @@ steps: run: ../command_line_tools/sequence_qc/0.2.4/sequence_qc_0.2.4.cwl 'sbg:x': 353.515625 'sbg:y': 1426.328125 - - id: biometrics_extract_0_2_14 + - id: biometrics_extract_0_2_15 in: - id: sample_bam source: duplex_bam @@ -405,15 +405,15 @@ steps: source: duplex_biometrics_extract_file_type out: - id: biometrics_extract_pickle - run: ../command_line_tools/biometrics_extract/0.2.14/biometrics_extract.cwl + run: ../command_line_tools/biometrics_extract/0.2.15/biometrics_extract.cwl 'sbg:x': 353.515625 'sbg:y': 1616.984375 - - id: biometrics_minor_0_2_14 + - id: biometrics_minor_0_2_15 in: - id: input linkMerge: merge_nested source: - - biometrics_extract_0_2_14/biometrics_extract_pickle + - biometrics_extract_0_2_15/biometrics_extract_pickle - id: prefix default: duplex source: prefix @@ -427,7 +427,7 @@ steps: - id: biometrics_minor_json - id: biometrics_minor_plot - id: biometrics_minor_sites_plot - run: ../command_line_tools/biometrics_minor/0.2.14/biometrics_minor.cwl + run: ../command_line_tools/biometrics_minor/0.2.15/biometrics_minor.cwl 'sbg:x': 984.2216796875 'sbg:y': 2265.96875 - id: getbasecountsmultisample_1_2_5 From 7d1ab56aed688a68f3a4b66e641d09faa2580264 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Mon, 17 Jun 2024 23:26:34 -0400 Subject: [PATCH 14/19] Update actions --- .github/workflows/codeql.yml | 2 +- .github/workflows/pack_cwls.yml | 6 +++--- .github/workflows/validate_cwls.yml | 6 +++--- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index b54befb..165da10 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -24,7 +24,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Initialize CodeQL uses: github/codeql-action/init@v2 diff --git a/.github/workflows/pack_cwls.yml b/.github/workflows/pack_cwls.yml index 6f48c0c..c813ad3 100644 --- a/.github/workflows/pack_cwls.yml +++ b/.github/workflows/pack_cwls.yml @@ -14,13 +14,13 @@ jobs: strategy: fail-fast: false matrix: - python-version: [3.7, 3.8, 3.9] + python-version: [3.7.x, 3.8.x, 3.9.x] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 with: submodules: recursive - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install cwltool diff --git a/.github/workflows/validate_cwls.yml b/.github/workflows/validate_cwls.yml index 1a677a9..a3629f5 100644 --- a/.github/workflows/validate_cwls.yml +++ b/.github/workflows/validate_cwls.yml @@ -12,13 +12,13 @@ jobs: strategy: fail-fast: false matrix: - python-version: [3.7, 3.8, 3.9] + python-version: [3.7.x, 3.8.x, 3.9.x] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 with: submodules: recursive - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install cwltool From 8d0d403a06ab8c50723256585dce5157a79da08a Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Tue, 18 Jun 2024 03:28:38 +0000 Subject: [PATCH 15/19] Commit from GitHub Actions --- .../qc_collapsed_bam_v2.0__packed.cwl | 168 +++++++++--------- qc_duplex_bam/qc_duplex_bam_v2.0__packed.cwl | 118 ++++++------ 2 files changed, 143 insertions(+), 143 deletions(-) diff --git a/qc_collapsed_bam/qc_collapsed_bam_v2.0__packed.cwl b/qc_collapsed_bam/qc_collapsed_bam_v2.0__packed.cwl index dbacdfd..53b8885 100755 --- a/qc_collapsed_bam/qc_collapsed_bam_v2.0__packed.cwl +++ b/qc_collapsed_bam/qc_collapsed_bam_v2.0__packed.cwl @@ -314,7 +314,7 @@ ], "inputs": [ { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/sample_bam", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/sample_bam", "type": "File", "inputBinding": { "position": 0, @@ -326,7 +326,7 @@ ] }, { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/sample_sex", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/sample_sex", "type": [ "null", "string" @@ -338,7 +338,7 @@ "doc": "Expected sample sex (i.e. M or F)." }, { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/sample_group", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/sample_group", "type": [ "null", "string" @@ -350,7 +350,7 @@ "doc": "The sample group (e.g. the sample patient ID)." }, { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/sample_name", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/sample_name", "type": "string", "inputBinding": { "position": 0, @@ -359,7 +359,7 @@ "doc": "Sample name. If not specified, sample name is automatically figured out from the BAM file." }, { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/fafile", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/fafile", "type": "File", "inputBinding": { "position": 0, @@ -371,7 +371,7 @@ ] }, { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/vcf_file", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/vcf_file", "type": "File", "inputBinding": { "position": 0, @@ -380,7 +380,7 @@ "doc": "VCF file containing the SNPs to be queried." }, { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/bed_file", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/bed_file", "type": [ "null", "File" @@ -392,7 +392,7 @@ "doc": "BED file containing the intervals to be queried." }, { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/database", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/database", "type": [ "null", "string" @@ -405,7 +405,7 @@ }, { "default": 1, - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/min_mapping_quality", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/min_mapping_quality", "type": [ "null", "int" @@ -418,7 +418,7 @@ }, { "default": 1, - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/min_base_quality", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/min_base_quality", "type": [ "null", "int" @@ -431,7 +431,7 @@ }, { "default": 10, - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/min_coverage", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/min_coverage", "type": [ "null", "int" @@ -444,7 +444,7 @@ }, { "default": 0.1, - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/min_homozygous_thresh", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/min_homozygous_thresh", "type": [ "null", "float" @@ -456,7 +456,7 @@ "doc": "Minimum threshold to define homozygous." }, { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/default_genotype", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/default_genotype", "type": [ "null", "string" @@ -468,7 +468,7 @@ "doc": "Default genotype if coverage is too low (options are Het or Hom)." }, { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/file_type", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/file_type", "type": [ "null", "string" @@ -478,7 +478,7 @@ ], "outputs": [ { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/biometrics_extract_pickle", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/biometrics_extract_pickle", "type": "File", "outputBinding": { "glob": "${\n if (inputs.database) {\n return inputs.database + '/' + inputs.sample_name + '.pickle';\n }\n else {\n return inputs.sample_name + '.pickle';\n }\n}", @@ -494,7 +494,7 @@ }, { "class": "DockerRequirement", - "dockerPull": "ghcr.io/msk-access/biometrics:0.2.14" + "dockerPull": "ghcr.io/msk-access/biometrics:0.2.15" }, { "class": "InlineJavascriptRequirement" @@ -529,8 +529,8 @@ "http://xmlns.com/foaf/0.1/member": [ { "class": "http://xmlns.com/foaf/0.1/Person", - "http://xmlns.com/foaf/0.1/mbox": "mailto:murphyc4@mskcc.org", - "http://xmlns.com/foaf/0.1/name": "Charlie Murphy" + "http://xmlns.com/foaf/0.1/mbox": "mailto:shahr2@mskcc.org", + "http://xmlns.com/foaf/0.1/name": "Ronak Shah" } ], "http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center" @@ -540,7 +540,7 @@ { "class": "http://usefulinc.com/ns/doap#Version", "http://usefulinc.com/ns/doap#name": "biometrics", - "http://usefulinc.com/ns/doap#revision": "0.2.14" + "http://usefulinc.com/ns/doap#revision": "0.2.15" } ] }, @@ -553,7 +553,7 @@ ], "inputs": [ { - "id": "#biometrics_major.cwl/biometrics_major_0_2_14/input", + "id": "#biometrics_major.cwl/biometrics_major_0_2_15/input", "type": { "type": "array", "items": "File", @@ -567,7 +567,7 @@ "doc": "Can be one of three types: (1) path to a CSV file containing sample information (one per line). For example: sample_name,sample_bam,sample_type,sample_sex,sample_group. (2) Path to a '*.pk' file that was produced by the 'extract' tool. (3) Name of the sample to analyze; this assumes there is a file named '{sample_name}.pk' in your database directory. Can be specified more than once." }, { - "id": "#biometrics_major.cwl/biometrics_major_0_2_14/database", + "id": "#biometrics_major.cwl/biometrics_major_0_2_15/database", "type": [ "null", "string" @@ -580,7 +580,7 @@ }, { "default": 0.6, - "id": "#biometrics_major.cwl/biometrics_major_0_2_14/major_threshold", + "id": "#biometrics_major.cwl/biometrics_major_0_2_15/major_threshold", "type": [ "null", "float" @@ -592,7 +592,7 @@ "doc": "Major contamination threshold for bad sample." }, { - "id": "#biometrics_major.cwl/biometrics_major_0_2_14/prefix", + "id": "#biometrics_major.cwl/biometrics_major_0_2_15/prefix", "type": [ "null", "string" @@ -604,7 +604,7 @@ "doc": "Output file prefix." }, { - "id": "#biometrics_major.cwl/biometrics_major_0_2_14/plot", + "id": "#biometrics_major.cwl/biometrics_major_0_2_15/plot", "type": [ "null", "boolean" @@ -616,7 +616,7 @@ "doc": "Also output plots of the data." }, { - "id": "#biometrics_major.cwl/biometrics_major_0_2_14/json", + "id": "#biometrics_major.cwl/biometrics_major_0_2_15/json", "type": [ "null", "boolean" @@ -628,7 +628,7 @@ "doc": "Also output data in JSON format." }, { - "id": "#biometrics_major.cwl/biometrics_major_0_2_14/no_db_comparison", + "id": "#biometrics_major.cwl/biometrics_major_0_2_15/no_db_comparison", "type": [ "null", "boolean" @@ -642,14 +642,14 @@ ], "outputs": [ { - "id": "#biometrics_major.cwl/biometrics_major_0_2_14/biometrics_major_csv", + "id": "#biometrics_major.cwl/biometrics_major_0_2_15/biometrics_major_csv", "type": "File", "outputBinding": { "glob": "${\n if (inputs.prefix) {\n return inputs.prefix + '_major_contamination.csv'\n } else {\n return 'major_contamination.csv'\n }\n}" } }, { - "id": "#biometrics_major.cwl/biometrics_major_0_2_14/biometrics_major_json", + "id": "#biometrics_major.cwl/biometrics_major_0_2_15/biometrics_major_json", "type": [ "null", "File" @@ -659,7 +659,7 @@ } }, { - "id": "#biometrics_major.cwl/biometrics_major_0_2_14/biometrics_major_plot", + "id": "#biometrics_major.cwl/biometrics_major_0_2_15/biometrics_major_plot", "type": [ "null", "File" @@ -677,7 +677,7 @@ }, { "class": "DockerRequirement", - "dockerPull": "ghcr.io/msk-access/biometrics:0.2.14" + "dockerPull": "ghcr.io/msk-access/biometrics:0.2.15" }, { "class": "InlineJavascriptRequirement" @@ -713,7 +713,7 @@ { "class": "http://usefulinc.com/ns/doap#Version", "http://usefulinc.com/ns/doap#name": "biometrics", - "http://usefulinc.com/ns/doap#revision": "0.2.14" + "http://usefulinc.com/ns/doap#revision": "0.2.15" } ] }, @@ -726,7 +726,7 @@ ], "inputs": [ { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/input", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/input", "type": { "type": "array", "items": "File", @@ -740,7 +740,7 @@ "doc": "Can be one of three types: (1) path to a CSV file containing sample information (one per line). For example: sample_name,sample_bam,sample_type,sample_sex,sample_group. (2) Path to a '*.pk' file that was produced by the 'extract' tool. (3) Name of the sample to analyze; this assumes there is a file named '{sample_name}.pk' in your database directory. Can be specified more than once." }, { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/database", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/database", "type": [ "null", "string" @@ -753,7 +753,7 @@ }, { "default": 0.002, - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/minor_threshold", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/minor_threshold", "type": [ "null", "float" @@ -765,7 +765,7 @@ "doc": "Minor contamination threshold for bad sample." }, { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/prefix", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/prefix", "type": [ "null", "string" @@ -777,7 +777,7 @@ "doc": "Output file prefix." }, { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/plot", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/plot", "type": [ "null", "boolean" @@ -789,7 +789,7 @@ "doc": "Also output plots of the data." }, { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/json", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/json", "type": [ "null", "boolean" @@ -801,7 +801,7 @@ "doc": "Also output data in JSON format." }, { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/no_db_comparison", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/no_db_comparison", "type": [ "null", "boolean" @@ -815,14 +815,14 @@ ], "outputs": [ { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/biometrics_minor_csv", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/biometrics_minor_csv", "type": "File", "outputBinding": { "glob": "${\n if (inputs.prefix) {\n return inputs.prefix + '_minor_contamination.csv'\n } else {\n return 'minor_contamination.csv'\n }\n}" } }, { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/biometrics_minor_json", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/biometrics_minor_json", "type": [ "null", "File" @@ -832,7 +832,7 @@ } }, { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/biometrics_minor_plot", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/biometrics_minor_plot", "type": [ "null", "File" @@ -842,7 +842,7 @@ } }, { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/biometrics_minor_sites_plot", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/biometrics_minor_sites_plot", "type": [ "null", "File" @@ -860,7 +860,7 @@ }, { "class": "DockerRequirement", - "dockerPull": "ghcr.io/msk-access/biometrics:0.2.14" + "dockerPull": "ghcr.io/msk-access/biometrics:0.2.15" }, { "class": "InlineJavascriptRequirement" @@ -885,8 +885,8 @@ "http://xmlns.com/foaf/0.1/member": [ { "class": "http://xmlns.com/foaf/0.1/Person", - "http://xmlns.com/foaf/0.1/mbox": "mailto:murphyc4@mskcc.org", - "http://xmlns.com/foaf/0.1/name": "Charlie Murphy" + "http://xmlns.com/foaf/0.1/mbox": "mailto:shahr2@mskcc.org", + "http://xmlns.com/foaf/0.1/name": "Ronak Shah" } ], "http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center" @@ -896,7 +896,7 @@ { "class": "http://usefulinc.com/ns/doap#Version", "http://usefulinc.com/ns/doap#name": "biometrics", - "http://usefulinc.com/ns/doap#revision": "0.2.14" + "http://usefulinc.com/ns/doap#revision": "0.2.15" } ] }, @@ -909,7 +909,7 @@ ], "inputs": [ { - "id": "#biometrics_sexmismatch.cwl/biometrics_sexmismatch_0_2_14/input", + "id": "#biometrics_sexmismatch.cwl/biometrics_sexmismatch_0_2_15/input", "type": { "type": "array", "items": "File", @@ -923,7 +923,7 @@ "doc": "Can be one of three types: (1) path to a CSV file containing sample information (one per line). For example: sample_name,sample_bam,sample_type,sample_sex,sample_group. (2) Path to a '*.pk' file that was produced by the 'extract' tool. (3) Name of the sample to analyze; this assumes there is a file named '{sample_name}.pk' in your database directory. Can be specified more than once." }, { - "id": "#biometrics_sexmismatch.cwl/biometrics_sexmismatch_0_2_14/database", + "id": "#biometrics_sexmismatch.cwl/biometrics_sexmismatch_0_2_15/database", "type": [ "null", "string" @@ -936,7 +936,7 @@ }, { "default": 50, - "id": "#biometrics_sexmismatch.cwl/biometrics_sexmismatch_0_2_14/coverage_threshold", + "id": "#biometrics_sexmismatch.cwl/biometrics_sexmismatch_0_2_15/coverage_threshold", "type": [ "null", "int" @@ -948,7 +948,7 @@ "doc": "Samples with Y chromosome above this value will be considered male." }, { - "id": "#biometrics_sexmismatch.cwl/biometrics_sexmismatch_0_2_14/prefix", + "id": "#biometrics_sexmismatch.cwl/biometrics_sexmismatch_0_2_15/prefix", "type": [ "null", "string" @@ -960,7 +960,7 @@ "doc": "Output file prefix." }, { - "id": "#biometrics_sexmismatch.cwl/biometrics_sexmismatch_0_2_14/json", + "id": "#biometrics_sexmismatch.cwl/biometrics_sexmismatch_0_2_15/json", "type": [ "null", "boolean" @@ -972,7 +972,7 @@ "doc": "Also output data in JSON format." }, { - "id": "#biometrics_sexmismatch.cwl/biometrics_sexmismatch_0_2_14/no_db_comparison", + "id": "#biometrics_sexmismatch.cwl/biometrics_sexmismatch_0_2_15/no_db_comparison", "type": [ "null", "boolean" @@ -986,14 +986,14 @@ ], "outputs": [ { - "id": "#biometrics_sexmismatch.cwl/biometrics_sexmismatch_0_2_14/biometrics_sexmismatch_csv", + "id": "#biometrics_sexmismatch.cwl/biometrics_sexmismatch_0_2_15/biometrics_sexmismatch_csv", "type": "File", "outputBinding": { "glob": "${\n if (inputs.prefix) {\n return inputs.prefix + '_sex_mismatch.csv'\n } else {\n return 'sex_mismatch.csv'\n }\n}" } }, { - "id": "#biometrics_sexmismatch.cwl/biometrics_sexmismatch_0_2_14/biometrics_sexmismatch_json", + "id": "#biometrics_sexmismatch.cwl/biometrics_sexmismatch_0_2_15/biometrics_sexmismatch_json", "type": [ "null", "File" @@ -1011,7 +1011,7 @@ }, { "class": "DockerRequirement", - "dockerPull": "ghcr.io/msk-access/biometrics:0.2.14" + "dockerPull": "ghcr.io/msk-access/biometrics:0.2.15" }, { "class": "InlineJavascriptRequirement" @@ -1036,8 +1036,8 @@ "http://xmlns.com/foaf/0.1/member": [ { "class": "http://xmlns.com/foaf/0.1/Person", - "http://xmlns.com/foaf/0.1/mbox": "mailto:murphyc4@mskcc.org", - "http://xmlns.com/foaf/0.1/name": "Charlie Murphy" + "http://xmlns.com/foaf/0.1/mbox": "mailto:shahr2@mskcc.org", + "http://xmlns.com/foaf/0.1/name": "Ronak Shah" } ], "http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center" @@ -1047,7 +1047,7 @@ { "class": "http://usefulinc.com/ns/doap#Version", "http://usefulinc.com/ns/doap#name": "biometrics", - "http://usefulinc.com/ns/doap#revision": "0.2.14" + "http://usefulinc.com/ns/doap#revision": "0.2.15" } ] }, @@ -3056,7 +3056,7 @@ { "id": "#main/biometrics_major_plot", "outputSource": [ - "#main/biometrics_major_0_2_14/biometrics_major_plot" + "#main/biometrics_major_0_2_15/biometrics_major_plot" ], "type": [ "null", @@ -3068,7 +3068,7 @@ { "id": "#main/biometrics_major_json", "outputSource": [ - "#main/biometrics_major_0_2_14/biometrics_major_json" + "#main/biometrics_major_0_2_15/biometrics_major_json" ], "type": [ "null", @@ -3080,7 +3080,7 @@ { "id": "#main/biometrics_major_csv", "outputSource": [ - "#main/biometrics_major_0_2_14/biometrics_major_csv" + "#main/biometrics_major_0_2_15/biometrics_major_csv" ], "type": "File", "https://www.sevenbridges.com/x": 1482.3623046875, @@ -3089,7 +3089,7 @@ { "id": "#main/collapsed_biometrics_extract_pickle", "outputSource": [ - "#main/biometrics_extract_0_2_14/biometrics_extract_pickle" + "#main/biometrics_extract_0_2_15/biometrics_extract_pickle" ], "type": "File", "https://www.sevenbridges.com/x": 982.1435546875, @@ -3209,7 +3209,7 @@ "id": "#main/biometrics_minor/input", "linkMerge": "merge_nested", "source": [ - "#main/biometrics_extract_0_2_14/biometrics_extract_pickle" + "#main/biometrics_extract_0_2_15/biometrics_extract_pickle" ] }, { @@ -3257,7 +3257,7 @@ "id": "#main/biometrics_sexmismatch/input", "linkMerge": "merge_flattened", "source": [ - "#main/biometrics_extract_0_2_14/biometrics_extract_pickle" + "#main/biometrics_extract_0_2_15/biometrics_extract_pickle" ] }, { @@ -3288,43 +3288,43 @@ "https://www.sevenbridges.com/y": 1760.875 }, { - "id": "#main/biometrics_major_0_2_14", + "id": "#main/biometrics_major_0_2_15", "in": [ { - "id": "#main/biometrics_major_0_2_14/input", + "id": "#main/biometrics_major_0_2_15/input", "linkMerge": "merge_nested", "source": [ - "#main/biometrics_extract_0_2_14/biometrics_extract_pickle" + "#main/biometrics_extract_0_2_15/biometrics_extract_pickle" ] }, { - "id": "#main/biometrics_major_0_2_14/major_threshold", + "id": "#main/biometrics_major_0_2_15/major_threshold", "source": "#main/major_threshold" }, { - "id": "#main/biometrics_major_0_2_14/prefix", + "id": "#main/biometrics_major_0_2_15/prefix", "default": "collapsed", "source": "#main/prefix" }, { - "id": "#main/biometrics_major_0_2_14/plot", + "id": "#main/biometrics_major_0_2_15/plot", "source": "#main/plot" }, { - "id": "#main/biometrics_major_0_2_14/json", + "id": "#main/biometrics_major_0_2_15/json", "default": true, "source": "#main/json" } ], "out": [ { - "id": "#main/biometrics_major_0_2_14/biometrics_major_csv" + "id": "#main/biometrics_major_0_2_15/biometrics_major_csv" }, { - "id": "#main/biometrics_major_0_2_14/biometrics_major_json" + "id": "#main/biometrics_major_0_2_15/biometrics_major_json" }, { - "id": "#main/biometrics_major_0_2_14/biometrics_major_plot" + "id": "#main/biometrics_major_0_2_15/biometrics_major_plot" } ], "run": "#biometrics_major.cwl", @@ -3332,45 +3332,45 @@ "https://www.sevenbridges.com/y": 2079.625 }, { - "id": "#main/biometrics_extract_0_2_14", + "id": "#main/biometrics_extract_0_2_15", "in": [ { - "id": "#main/biometrics_extract_0_2_14/sample_bam", + "id": "#main/biometrics_extract_0_2_15/sample_bam", "source": "#main/collapsed_bam" }, { - "id": "#main/biometrics_extract_0_2_14/sample_sex", + "id": "#main/biometrics_extract_0_2_15/sample_sex", "source": "#main/sample_sex" }, { - "id": "#main/biometrics_extract_0_2_14/sample_group", + "id": "#main/biometrics_extract_0_2_15/sample_group", "source": "#main/sample_group" }, { - "id": "#main/biometrics_extract_0_2_14/sample_name", + "id": "#main/biometrics_extract_0_2_15/sample_name", "source": "#main/sample_name" }, { - "id": "#main/biometrics_extract_0_2_14/fafile", + "id": "#main/biometrics_extract_0_2_15/fafile", "source": "#main/reference" }, { - "id": "#main/biometrics_extract_0_2_14/vcf_file", + "id": "#main/biometrics_extract_0_2_15/vcf_file", "source": "#main/vcf_file" }, { - "id": "#main/biometrics_extract_0_2_14/bed_file", + "id": "#main/biometrics_extract_0_2_15/bed_file", "source": "#main/bed_file" }, { - "id": "#main/biometrics_extract_0_2_14/file_type", + "id": "#main/biometrics_extract_0_2_15/file_type", "default": "collapsed", "source": "#main/collapsed_biometrics_extract_file_type" } ], "out": [ { - "id": "#main/biometrics_extract_0_2_14/biometrics_extract_pickle" + "id": "#main/biometrics_extract_0_2_15/biometrics_extract_pickle" } ], "run": "#biometrics_extract.cwl", diff --git a/qc_duplex_bam/qc_duplex_bam_v2.0__packed.cwl b/qc_duplex_bam/qc_duplex_bam_v2.0__packed.cwl index 265204b..14a1089 100644 --- a/qc_duplex_bam/qc_duplex_bam_v2.0__packed.cwl +++ b/qc_duplex_bam/qc_duplex_bam_v2.0__packed.cwl @@ -314,7 +314,7 @@ ], "inputs": [ { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/sample_bam", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/sample_bam", "type": "File", "inputBinding": { "position": 0, @@ -326,7 +326,7 @@ ] }, { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/sample_sex", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/sample_sex", "type": [ "null", "string" @@ -338,7 +338,7 @@ "doc": "Expected sample sex (i.e. M or F)." }, { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/sample_group", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/sample_group", "type": [ "null", "string" @@ -350,7 +350,7 @@ "doc": "The sample group (e.g. the sample patient ID)." }, { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/sample_name", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/sample_name", "type": "string", "inputBinding": { "position": 0, @@ -359,7 +359,7 @@ "doc": "Sample name. If not specified, sample name is automatically figured out from the BAM file." }, { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/fafile", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/fafile", "type": "File", "inputBinding": { "position": 0, @@ -371,7 +371,7 @@ ] }, { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/vcf_file", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/vcf_file", "type": "File", "inputBinding": { "position": 0, @@ -380,7 +380,7 @@ "doc": "VCF file containing the SNPs to be queried." }, { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/bed_file", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/bed_file", "type": [ "null", "File" @@ -392,7 +392,7 @@ "doc": "BED file containing the intervals to be queried." }, { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/database", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/database", "type": [ "null", "string" @@ -405,7 +405,7 @@ }, { "default": 1, - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/min_mapping_quality", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/min_mapping_quality", "type": [ "null", "int" @@ -418,7 +418,7 @@ }, { "default": 1, - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/min_base_quality", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/min_base_quality", "type": [ "null", "int" @@ -431,7 +431,7 @@ }, { "default": 10, - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/min_coverage", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/min_coverage", "type": [ "null", "int" @@ -444,7 +444,7 @@ }, { "default": 0.1, - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/min_homozygous_thresh", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/min_homozygous_thresh", "type": [ "null", "float" @@ -456,7 +456,7 @@ "doc": "Minimum threshold to define homozygous." }, { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/default_genotype", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/default_genotype", "type": [ "null", "string" @@ -468,7 +468,7 @@ "doc": "Default genotype if coverage is too low (options are Het or Hom)." }, { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/file_type", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/file_type", "type": [ "null", "string" @@ -478,7 +478,7 @@ ], "outputs": [ { - "id": "#biometrics_extract.cwl/biometrics_extract_0_2_14/biometrics_extract_pickle", + "id": "#biometrics_extract.cwl/biometrics_extract_0_2_15/biometrics_extract_pickle", "type": "File", "outputBinding": { "glob": "${\n if (inputs.database) {\n return inputs.database + '/' + inputs.sample_name + '.pickle';\n }\n else {\n return inputs.sample_name + '.pickle';\n }\n}", @@ -494,7 +494,7 @@ }, { "class": "DockerRequirement", - "dockerPull": "ghcr.io/msk-access/biometrics:0.2.14" + "dockerPull": "ghcr.io/msk-access/biometrics:0.2.15" }, { "class": "InlineJavascriptRequirement" @@ -529,8 +529,8 @@ "http://xmlns.com/foaf/0.1/member": [ { "class": "http://xmlns.com/foaf/0.1/Person", - "http://xmlns.com/foaf/0.1/mbox": "mailto:murphyc4@mskcc.org", - "http://xmlns.com/foaf/0.1/name": "Charlie Murphy" + "http://xmlns.com/foaf/0.1/mbox": "mailto:shahr2@mskcc.org", + "http://xmlns.com/foaf/0.1/name": "Ronak Shah" } ], "http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center" @@ -540,7 +540,7 @@ { "class": "http://usefulinc.com/ns/doap#Version", "http://usefulinc.com/ns/doap#name": "biometrics", - "http://usefulinc.com/ns/doap#revision": "0.2.14" + "http://usefulinc.com/ns/doap#revision": "0.2.15" } ] }, @@ -553,7 +553,7 @@ ], "inputs": [ { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/input", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/input", "type": { "type": "array", "items": "File", @@ -567,7 +567,7 @@ "doc": "Can be one of three types: (1) path to a CSV file containing sample information (one per line). For example: sample_name,sample_bam,sample_type,sample_sex,sample_group. (2) Path to a '*.pk' file that was produced by the 'extract' tool. (3) Name of the sample to analyze; this assumes there is a file named '{sample_name}.pk' in your database directory. Can be specified more than once." }, { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/database", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/database", "type": [ "null", "string" @@ -580,7 +580,7 @@ }, { "default": 0.002, - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/minor_threshold", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/minor_threshold", "type": [ "null", "float" @@ -592,7 +592,7 @@ "doc": "Minor contamination threshold for bad sample." }, { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/prefix", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/prefix", "type": [ "null", "string" @@ -604,7 +604,7 @@ "doc": "Output file prefix." }, { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/plot", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/plot", "type": [ "null", "boolean" @@ -616,7 +616,7 @@ "doc": "Also output plots of the data." }, { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/json", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/json", "type": [ "null", "boolean" @@ -628,7 +628,7 @@ "doc": "Also output data in JSON format." }, { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/no_db_comparison", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/no_db_comparison", "type": [ "null", "boolean" @@ -642,14 +642,14 @@ ], "outputs": [ { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/biometrics_minor_csv", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/biometrics_minor_csv", "type": "File", "outputBinding": { "glob": "${\n if (inputs.prefix) {\n return inputs.prefix + '_minor_contamination.csv'\n } else {\n return 'minor_contamination.csv'\n }\n}" } }, { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/biometrics_minor_json", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/biometrics_minor_json", "type": [ "null", "File" @@ -659,7 +659,7 @@ } }, { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/biometrics_minor_plot", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/biometrics_minor_plot", "type": [ "null", "File" @@ -669,7 +669,7 @@ } }, { - "id": "#biometrics_minor.cwl/biometrics_minor_0_2_14/biometrics_minor_sites_plot", + "id": "#biometrics_minor.cwl/biometrics_minor_0_2_15/biometrics_minor_sites_plot", "type": [ "null", "File" @@ -687,7 +687,7 @@ }, { "class": "DockerRequirement", - "dockerPull": "ghcr.io/msk-access/biometrics:0.2.14" + "dockerPull": "ghcr.io/msk-access/biometrics:0.2.15" }, { "class": "InlineJavascriptRequirement" @@ -712,8 +712,8 @@ "http://xmlns.com/foaf/0.1/member": [ { "class": "http://xmlns.com/foaf/0.1/Person", - "http://xmlns.com/foaf/0.1/mbox": "mailto:murphyc4@mskcc.org", - "http://xmlns.com/foaf/0.1/name": "Charlie Murphy" + "http://xmlns.com/foaf/0.1/mbox": "mailto:shahr2@mskcc.org", + "http://xmlns.com/foaf/0.1/name": "Ronak Shah" } ], "http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center" @@ -723,7 +723,7 @@ { "class": "http://usefulinc.com/ns/doap#Version", "http://usefulinc.com/ns/doap#name": "biometrics", - "http://usefulinc.com/ns/doap#revision": "0.2.14" + "http://usefulinc.com/ns/doap#revision": "0.2.15" } ] }, @@ -2806,7 +2806,7 @@ { "id": "#main/duplex_biometrics_extract_pickle", "outputSource": [ - "#main/biometrics_extract_0_2_14/biometrics_extract_pickle" + "#main/biometrics_extract_0_2_15/biometrics_extract_pickle" ], "type": "File", "https://www.sevenbridges.com/x": 984.2216796875, @@ -2815,7 +2815,7 @@ { "id": "#main/biometrics_minor_sites_plot", "outputSource": [ - "#main/biometrics_minor_0_2_14/biometrics_minor_sites_plot" + "#main/biometrics_minor_0_2_15/biometrics_minor_sites_plot" ], "type": [ "null", @@ -2827,7 +2827,7 @@ { "id": "#main/biometrics_minor_plot", "outputSource": [ - "#main/biometrics_minor_0_2_14/biometrics_minor_plot" + "#main/biometrics_minor_0_2_15/biometrics_minor_plot" ], "type": [ "null", @@ -2839,7 +2839,7 @@ { "id": "#main/biometrics_minor_json", "outputSource": [ - "#main/biometrics_minor_0_2_14/biometrics_minor_json" + "#main/biometrics_minor_0_2_15/biometrics_minor_json" ], "type": [ "null", @@ -2851,7 +2851,7 @@ { "id": "#main/biometrics_minor_csv", "outputSource": [ - "#main/biometrics_minor_0_2_14/biometrics_minor_csv" + "#main/biometrics_minor_0_2_15/biometrics_minor_csv" ], "type": "File", "https://www.sevenbridges.com/x": 1432.8466796875, @@ -3036,45 +3036,45 @@ "https://www.sevenbridges.com/y": 1426.328125 }, { - "id": "#main/biometrics_extract_0_2_14", + "id": "#main/biometrics_extract_0_2_15", "in": [ { - "id": "#main/biometrics_extract_0_2_14/sample_bam", + "id": "#main/biometrics_extract_0_2_15/sample_bam", "source": "#main/duplex_bam" }, { - "id": "#main/biometrics_extract_0_2_14/sample_sex", + "id": "#main/biometrics_extract_0_2_15/sample_sex", "source": "#main/sample_sex" }, { - "id": "#main/biometrics_extract_0_2_14/sample_group", + "id": "#main/biometrics_extract_0_2_15/sample_group", "source": "#main/sample_group" }, { - "id": "#main/biometrics_extract_0_2_14/sample_name", + "id": "#main/biometrics_extract_0_2_15/sample_name", "source": "#main/sample_name" }, { - "id": "#main/biometrics_extract_0_2_14/fafile", + "id": "#main/biometrics_extract_0_2_15/fafile", "source": "#main/reference" }, { - "id": "#main/biometrics_extract_0_2_14/vcf_file", + "id": "#main/biometrics_extract_0_2_15/vcf_file", "source": "#main/vcf_file" }, { - "id": "#main/biometrics_extract_0_2_14/min_coverage", + "id": "#main/biometrics_extract_0_2_15/min_coverage", "default": 200 }, { - "id": "#main/biometrics_extract_0_2_14/file_type", + "id": "#main/biometrics_extract_0_2_15/file_type", "default": "duplex", "source": "#main/duplex_biometrics_extract_file_type" } ], "out": [ { - "id": "#main/biometrics_extract_0_2_14/biometrics_extract_pickle" + "id": "#main/biometrics_extract_0_2_15/biometrics_extract_pickle" } ], "run": "#biometrics_extract.cwl", @@ -3082,42 +3082,42 @@ "https://www.sevenbridges.com/y": 1616.984375 }, { - "id": "#main/biometrics_minor_0_2_14", + "id": "#main/biometrics_minor_0_2_15", "in": [ { - "id": "#main/biometrics_minor_0_2_14/input", + "id": "#main/biometrics_minor_0_2_15/input", "linkMerge": "merge_nested", "source": [ - "#main/biometrics_extract_0_2_14/biometrics_extract_pickle" + "#main/biometrics_extract_0_2_15/biometrics_extract_pickle" ] }, { - "id": "#main/biometrics_minor_0_2_14/prefix", + "id": "#main/biometrics_minor_0_2_15/prefix", "default": "duplex", "source": "#main/prefix" }, { - "id": "#main/biometrics_minor_0_2_14/plot", + "id": "#main/biometrics_minor_0_2_15/plot", "source": "#main/plot" }, { - "id": "#main/biometrics_minor_0_2_14/json", + "id": "#main/biometrics_minor_0_2_15/json", "default": true, "source": "#main/json" } ], "out": [ { - "id": "#main/biometrics_minor_0_2_14/biometrics_minor_csv" + "id": "#main/biometrics_minor_0_2_15/biometrics_minor_csv" }, { - "id": "#main/biometrics_minor_0_2_14/biometrics_minor_json" + "id": "#main/biometrics_minor_0_2_15/biometrics_minor_json" }, { - "id": "#main/biometrics_minor_0_2_14/biometrics_minor_plot" + "id": "#main/biometrics_minor_0_2_15/biometrics_minor_plot" }, { - "id": "#main/biometrics_minor_0_2_14/biometrics_minor_sites_plot" + "id": "#main/biometrics_minor_0_2_15/biometrics_minor_sites_plot" } ], "run": "#biometrics_minor.cwl", From 9dad13d26a437641fbd15bce454c8198e44e86e1 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Mon, 17 Jun 2024 23:33:17 -0400 Subject: [PATCH 16/19] Update actions --- .github/workflows/pack_cwls.yml | 4 ++-- .github/workflows/validate_cwls.yml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/pack_cwls.yml b/.github/workflows/pack_cwls.yml index c813ad3..9c7b828 100644 --- a/.github/workflows/pack_cwls.yml +++ b/.github/workflows/pack_cwls.yml @@ -14,7 +14,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: [3.7.x, 3.8.x, 3.9.x] + python-version: [3.8.x, 3.9.x] steps: - uses: actions/checkout@v4 with: @@ -36,7 +36,7 @@ jobs: run: | echo Validating packed workflows... find . -name '*__packed.cwl' | xargs -I file cwltool --debug --validate file - - uses: EndBug/add-and-commit@v4 + - uses: EndBug/add-and-commit@v9.1.4 with: ref: ${{ github.head_ref }} env: diff --git a/.github/workflows/validate_cwls.yml b/.github/workflows/validate_cwls.yml index a3629f5..0b91458 100644 --- a/.github/workflows/validate_cwls.yml +++ b/.github/workflows/validate_cwls.yml @@ -12,7 +12,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: [3.7.x, 3.8.x, 3.9.x] + python-version: [3.8.x, 3.9.x] steps: - uses: actions/checkout@v4 with: @@ -24,7 +24,7 @@ jobs: - name: Install cwltool run: | python -m pip install toil[cwl]==5.7.1 - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Validate run: | pip install cwltool From 275a62872353456a2e39ce0605bc90dc101cfd6e Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Tue, 18 Jun 2024 00:19:11 -0400 Subject: [PATCH 17/19] Update command_line_tools --- command_line_tools | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/command_line_tools b/command_line_tools index d61c917..24accf3 160000 --- a/command_line_tools +++ b/command_line_tools @@ -1 +1 @@ -Subproject commit d61c9170bf84b35368eadfb3a522c6d143b93b55 +Subproject commit 24accf3747b8698a66b3ec262dc44f9a18231e8d From cfab797cb2f3794dc95de10121fe13a473156836 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Tue, 27 Aug 2024 10:44:26 -0400 Subject: [PATCH 18/19] Updating cores and mem --- command_line_tools | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/command_line_tools b/command_line_tools index 24accf3..7275e19 160000 --- a/command_line_tools +++ b/command_line_tools @@ -1 +1 @@ -Subproject commit 24accf3747b8698a66b3ec262dc44f9a18231e8d +Subproject commit 7275e19ae7e64331fbd3c4489e25cf0b2dcf124b From 6c948e78d226a1eb51affcd950616d1dc4f551e9 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Tue, 27 Aug 2024 10:45:55 -0400 Subject: [PATCH 19/19] Updating submodule to release branch --- command_line_tools | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/command_line_tools b/command_line_tools index 7275e19..082f3a3 160000 --- a/command_line_tools +++ b/command_line_tools @@ -1 +1 @@ -Subproject commit 7275e19ae7e64331fbd3c4489e25cf0b2dcf124b +Subproject commit 082f3a3177a845acfd717ad1783ae5b6a668095e