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Merge pull request #183 from msk-access/pv-update
Update run_processed_vardict.cwl
2 parents 5174e6c + 8ab29a3 commit 5f0b6ea

8 files changed

Lines changed: 122 additions & 20 deletions

‎qc_collapsed_bam/qc_collapsed_bam__packed.cwl‎

Lines changed: 20 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -466,14 +466,23 @@
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"prefix": "--default-genotype"
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},
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"doc": "Default genotype if coverage is too low (options are Het or Hom)."
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},
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{
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"id": "#biometrics_extract.cwl/biometrics_extract_0_2_13/file_type",
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"type": [
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"null",
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"string"
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],
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"doc": "Specify the type of bam file you are generating the pickle for to be incorporated in pickle file name (Myeloid_1_L001_duplex.pickle)"
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}
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],
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"outputs": [
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{
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"id": "#biometrics_extract.cwl/biometrics_extract_0_2_13/biometrics_extract_pickle",
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"type": "File",
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"outputBinding": {
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"glob": "${\n if (inputs.database) {\n return inputs.database + '/' + inputs.sample_name + '.pickle';\n } else {\n return inputs.sample_name + '.pickle';\n }\n}"
484+
"glob": "${\n if (inputs.database) {\n return inputs.database + '/' + inputs.sample_name + '.pickle';\n }\n else {\n return inputs.sample_name + '.pickle';\n }\n}",
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"outputEval": "${\n if (inputs.file_type) {\n self[0].basename = inputs.sample_name + '_' + inputs.file_type + \".pickle\";\n return self;\n }\n else {\n return self;\n }\n}"
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}
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}
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],
@@ -499,6 +508,16 @@
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"class": "http://xmlns.com/foaf/0.1/Person",
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"http://xmlns.com/foaf/0.1/mbox": "mailto:murphyc4@mskcc.org",
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"http://xmlns.com/foaf/0.1/name": "Charlie Murphy"
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},
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{
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"class": "http://xmlns.com/foaf/0.1/Person",
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"http://xmlns.com/foaf/0.1/mbox": "mailto:shahr2@mskcc.org",
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"http://xmlns.com/foaf/0.1/name": "Ronak Shah"
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},
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{
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"class": "http://xmlns.com/foaf/0.1/Person",
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"http://xmlns.com/foaf/0.1/mbox": "mailto:charlk@mskcc.org",
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"http://xmlns.com/foaf/0.1/name": "Carmelina Charlambous"
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}
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],
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"http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center"

‎qc_collapsed_bam/qc_collapsed_bam_v2.0__packed.cwl‎

Lines changed: 34 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -466,14 +466,23 @@
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"prefix": "--default-genotype"
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},
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"doc": "Default genotype if coverage is too low (options are Het or Hom)."
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},
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{
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"id": "#biometrics_extract.cwl/biometrics_extract_0_2_13/file_type",
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"type": [
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"null",
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"string"
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],
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"doc": "Specify the type of bam file you are generating the pickle for to be incorporated in pickle file name (Myeloid_1_L001_duplex.pickle)"
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}
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],
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"outputs": [
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{
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"id": "#biometrics_extract.cwl/biometrics_extract_0_2_13/biometrics_extract_pickle",
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"type": "File",
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"outputBinding": {
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"glob": "${\n if (inputs.database) {\n return inputs.database + '/' + inputs.sample_name + '.pickle';\n } else {\n return inputs.sample_name + '.pickle';\n }\n}"
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"glob": "${\n if (inputs.database) {\n return inputs.database + '/' + inputs.sample_name + '.pickle';\n }\n else {\n return inputs.sample_name + '.pickle';\n }\n}",
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"outputEval": "${\n if (inputs.file_type) {\n self[0].basename = inputs.sample_name + '_' + inputs.file_type + \".pickle\";\n return self;\n }\n else {\n return self;\n }\n}"
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}
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}
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],
@@ -499,6 +508,16 @@
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"class": "http://xmlns.com/foaf/0.1/Person",
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"http://xmlns.com/foaf/0.1/mbox": "mailto:murphyc4@mskcc.org",
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"http://xmlns.com/foaf/0.1/name": "Charlie Murphy"
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},
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{
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"class": "http://xmlns.com/foaf/0.1/Person",
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"http://xmlns.com/foaf/0.1/mbox": "mailto:shahr2@mskcc.org",
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"http://xmlns.com/foaf/0.1/name": "Ronak Shah"
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},
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{
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"class": "http://xmlns.com/foaf/0.1/Person",
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"http://xmlns.com/foaf/0.1/mbox": "mailto:charlk@mskcc.org",
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"http://xmlns.com/foaf/0.1/name": "Carmelina Charlambous"
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}
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],
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"http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center"
@@ -2743,6 +2762,15 @@
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],
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 1923.75
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},
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{
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"id": "#main/collapsed_biometrics_extract_file_type",
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"type": [
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"null",
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"string"
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],
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"https://www.sevenbridges.com/x": 723.521240234375,
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"https://www.sevenbridges.com/y": 1204.8056640625
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}
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],
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"outputs": [
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{
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"id": "#main/biometrics_extract_0_2_13/bed_file",
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"source": "#main/bed_file"
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},
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{
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"id": "#main/biometrics_extract_0_2_13/file_type",
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"default": "collapsed",
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"source": "#main/collapsed_biometrics_extract_file_type"
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}
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],
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"out": [
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"requirements": [
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{
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"class": "SubworkflowFeatureRequirement"
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},
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{
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"class": "InlineJavascriptRequirement"
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},
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{
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"class": "StepInputExpressionRequirement"
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}
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],
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"https://schema.org/author": [

‎qc_duplex_bam/qc_duplex_bam__packed.cwl‎

Lines changed: 20 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -466,14 +466,23 @@
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"prefix": "--default-genotype"
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},
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"doc": "Default genotype if coverage is too low (options are Het or Hom)."
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},
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{
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"id": "#biometrics_extract.cwl/biometrics_extract_0_2_13/file_type",
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"type": [
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"null",
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"string"
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],
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"doc": "Specify the type of bam file you are generating the pickle for to be incorporated in pickle file name (Myeloid_1_L001_duplex.pickle)"
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}
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],
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"outputs": [
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{
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"id": "#biometrics_extract.cwl/biometrics_extract_0_2_13/biometrics_extract_pickle",
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"type": "File",
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"outputBinding": {
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"glob": "${\n if (inputs.database) {\n return inputs.database + '/' + inputs.sample_name + '.pickle';\n } else {\n return inputs.sample_name + '.pickle';\n }\n}"
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"glob": "${\n if (inputs.database) {\n return inputs.database + '/' + inputs.sample_name + '.pickle';\n }\n else {\n return inputs.sample_name + '.pickle';\n }\n}",
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"outputEval": "${\n if (inputs.file_type) {\n self[0].basename = inputs.sample_name + '_' + inputs.file_type + \".pickle\";\n return self;\n }\n else {\n return self;\n }\n}"
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}
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}
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],
@@ -499,6 +508,16 @@
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"class": "http://xmlns.com/foaf/0.1/Person",
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"http://xmlns.com/foaf/0.1/mbox": "mailto:murphyc4@mskcc.org",
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"http://xmlns.com/foaf/0.1/name": "Charlie Murphy"
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},
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{
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"class": "http://xmlns.com/foaf/0.1/Person",
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"http://xmlns.com/foaf/0.1/mbox": "mailto:shahr2@mskcc.org",
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"http://xmlns.com/foaf/0.1/name": "Ronak Shah"
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},
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{
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"class": "http://xmlns.com/foaf/0.1/Person",
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"http://xmlns.com/foaf/0.1/mbox": "mailto:charlk@mskcc.org",
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"http://xmlns.com/foaf/0.1/name": "Carmelina Charlambous"
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}
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],
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"http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center"

‎qc_duplex_bam/qc_duplex_bam_v2.0__packed.cwl‎

Lines changed: 34 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -466,14 +466,23 @@
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"prefix": "--default-genotype"
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},
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"doc": "Default genotype if coverage is too low (options are Het or Hom)."
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},
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{
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"id": "#biometrics_extract.cwl/biometrics_extract_0_2_13/file_type",
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"type": [
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"null",
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"string"
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],
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"doc": "Specify the type of bam file you are generating the pickle for to be incorporated in pickle file name (Myeloid_1_L001_duplex.pickle)"
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}
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],
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"outputs": [
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{
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"id": "#biometrics_extract.cwl/biometrics_extract_0_2_13/biometrics_extract_pickle",
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"type": "File",
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"outputBinding": {
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"glob": "${\n if (inputs.database) {\n return inputs.database + '/' + inputs.sample_name + '.pickle';\n } else {\n return inputs.sample_name + '.pickle';\n }\n}"
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"glob": "${\n if (inputs.database) {\n return inputs.database + '/' + inputs.sample_name + '.pickle';\n }\n else {\n return inputs.sample_name + '.pickle';\n }\n}",
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"outputEval": "${\n if (inputs.file_type) {\n self[0].basename = inputs.sample_name + '_' + inputs.file_type + \".pickle\";\n return self;\n }\n else {\n return self;\n }\n}"
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}
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}
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],
@@ -499,6 +508,16 @@
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"class": "http://xmlns.com/foaf/0.1/Person",
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"http://xmlns.com/foaf/0.1/mbox": "mailto:murphyc4@mskcc.org",
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"http://xmlns.com/foaf/0.1/name": "Charlie Murphy"
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},
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{
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"class": "http://xmlns.com/foaf/0.1/Person",
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"http://xmlns.com/foaf/0.1/mbox": "mailto:shahr2@mskcc.org",
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"http://xmlns.com/foaf/0.1/name": "Ronak Shah"
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},
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{
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"class": "http://xmlns.com/foaf/0.1/Person",
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"http://xmlns.com/foaf/0.1/mbox": "mailto:charlk@mskcc.org",
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"http://xmlns.com/foaf/0.1/name": "Carmelina Charlambous"
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}
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],
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"http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center"
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"type": "int",
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 2667.265625
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},
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{
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"id": "#main/duplex_biometrics_extract_file_type",
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"type": [
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"null",
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"string"
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],
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"https://www.sevenbridges.com/x": 829.6761474609375,
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"https://www.sevenbridges.com/y": 1418.3421630859375
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}
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],
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"outputs": [
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{
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"id": "#main/biometrics_extract_0_2_13/min_coverage",
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"default": 200
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},
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{
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"id": "#main/biometrics_extract_0_2_13/file_type",
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"default": "duplex",
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"source": "#main/duplex_biometrics_extract_file_type"
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}
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],
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"out": [
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"requirements": [
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{
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"class": "SubworkflowFeatureRequirement"
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},
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{
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"class": "InlineJavascriptRequirement"
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},
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{
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"class": "StepInputExpressionRequirement"
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}
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],
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"https://schema.org/author": [

‎qc_uncollapsed_bam/qc_uncollapsed_bam__packed.cwl‎

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"type": "File",
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"outputBinding": {
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"glob": "${\n if(inputs.output){\n return inputs.output\n } else {\n return inputs.input.basename.replace(/.bam|.sam/, '_revertsam.bam')\n }\n}"
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}
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},
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"secondaryFiles": [
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"^.bai"
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]
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},
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{
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"id": "#gatk_revert_sam_4.1.8.0.cwl/gatk_revert_sam_4_1_8_0/gatk_revert_sam_output_map",

‎qc_uncollapsed_bam/qc_uncollapsed_bam_v2.0__packed.cwl‎

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"type": "File",
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"outputBinding": {
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"glob": "${\n if(inputs.output){\n return inputs.output\n } else {\n return inputs.input.basename.replace(/.bam|.sam/, '_revertsam.bam')\n }\n}"
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}
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},
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"secondaryFiles": [
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"^.bai"
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]
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},
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{
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"id": "#gatk_revert_sam_4.1.8.0.cwl/gatk_revert_sam_4_1_8_0/gatk_revert_sam_output_map",
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{
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"id": "#main/gatk_revert_sam_4_1_8_0/validation_stringency",
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"default": "SILENT"
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},
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{
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"id": "#main/gatk_revert_sam_4_1_8_0/create_index",
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"default": true
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}
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],
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"out": [

‎vardict_workflow/run_processed_vardict.cwl‎

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- id: vcf_complex
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- id: vcf
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run: >-
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../command_line_tools/postprocessing_variant_calls/0.1.4/pv_vardict_single_filter.cwl
106+
../command_line_tools/postprocessing_variant_calls/0.1.5/pv_vardict_single_filter.cwl
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'sbg:x': 1.4255318641662598
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'sbg:y': -197.1702117919922
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- id: variants_concat

‎vardict_workflow/run_processed_vardict__packed.cwl‎

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"hints": [
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{
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"class": "DockerRequirement",
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"dockerPull": "ghcr.io/msk-access/postprocessing_variant_calls:0.1.4"
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"dockerPull": "ghcr.io/msk-access/postprocessing_variant_calls:0.1.5"
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}
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],
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"id": "#pv_vardict_single_filter.cwl",

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