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‎variant_annotation/chipvar_processing__packed.cwl‎

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{
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"$graph": [
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{
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"class": "CommandLineTool",
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"id": "#maf_filter_cmoch.cwl",
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"baseCommand": [
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"pv"
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],
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"inputs": [
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{
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"id": "#maf_filter_cmoch.cwl/pv_maf_filter/memory_per_job",
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"type": [
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"null",
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"int"
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],
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"doc": "Memory per job in megabytes"
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},
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{
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"id": "#maf_filter_cmoch.cwl/pv_maf_filter/memory_overhead",
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"type": [
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"null",
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"int"
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],
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"doc": "Memory overhead per job in megabytes"
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},
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{
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"id": "#maf_filter_cmoch.cwl/pv_maf_filter/number_of_threads",
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"type": [
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"null",
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"int"
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]
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},
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{
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"id": "#maf_filter_cmoch.cwl/pv_maf_filter/input_maf",
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"type": "File",
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"inputBinding": {
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"position": 0,
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"prefix": "-m"
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}
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},
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{
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"id": "#maf_filter_cmoch.cwl/pv_maf_filter/output_maf_name",
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"type": [
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"null",
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"string"
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],
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"inputBinding": {
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"position": 0,
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"prefix": "-o"
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},
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"https://www.sevenbridges.com/toolDefaultValue": "output.maf"
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},
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{
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"id": "#maf_filter_cmoch.cwl/pv_maf_filter/output_maf_separator",
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"type": [
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"null",
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"string"
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],
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"inputBinding": {
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"prefix": "-sep"
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},
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"https://www.sevenbridges.com/toolDefaultValue": "tsv"
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}
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],
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"label": "pv_maf_filter",
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"arguments": [
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"maf",
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"filter",
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"cmo_ch",
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{
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"position": 2,
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"prefix": "--output",
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"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}"
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}
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],
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"requirements": [
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{
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"class": "ResourceRequirement",
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"ramMin": 8000,
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"coresMin": 2
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},
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{
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"class": "DockerRequirement",
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"dockerPull": "ghcr.io/msk-access/postprocessing_variant_calls:chipvar_dev10"
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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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"http://purl.org/dc/terms/contributor": [
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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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"http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center"
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}
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"http://purl.org/dc/terms/creator": [
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"class": "http://xmlns.com/foaf/0.1/Person",
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"http://xmlns.com/foaf/0.1/mbox": "mailto:sivaprk@mskcc.org",
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"http://xmlns.com/foaf/0.1/name": "Karthigayini Sivaprakasam"
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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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}
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"http://usefulinc.com/ns/doap#revision": "0.2.3"
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}
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"outputs": [
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{
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"id": "#maf_filter_cmoch.cwl/pv_maf_filter/output",
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"type": [
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"null",
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"File"
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],
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"outputBinding": {
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"glob": "${ \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}"
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}
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}
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]
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},
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{
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"class": "CommandLineTool",
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"id": "#maf_tag_cmoch.cwl",
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"baseCommand": [
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"pv"
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],
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"inputs": [
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{
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"id": "#maf_tag_cmoch.cwl/pv_maf_tag/memory_per_job",
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"type": [
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"null",
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"int"
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],
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"doc": "Memory per job in megabytes"
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},
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{
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"id": "#maf_tag_cmoch.cwl/pv_maf_tag/memory_overhead",
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"type": [
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"null",
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"int"
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],
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"doc": "Memory overhead per job in megabytes"
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},
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{
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"id": "#maf_tag_cmoch.cwl/pv_maf_tag/number_of_threads",
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"type": [
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"null",
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"int"
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]
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},
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{
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"id": "#maf_tag_cmoch.cwl/pv_maf_tag/input_maf",
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"type": "File",
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"inputBinding": {
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"position": 0,
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"prefix": "-m"
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}
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},
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{
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"id": "#maf_tag_cmoch.cwl/pv_maf_tag/output_maf_name",
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"type": [
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"null",
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},
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{
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"id": "#maf_tag_cmoch.cwl/pv_maf_tag/output_maf_separator",
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"type": [
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"string"
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],
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"prefix": "-sep"
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},
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"https://www.sevenbridges.com/toolDefaultValue": "tsv"
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}
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],
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"outputs": [
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{
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"id": "#maf_tag_cmoch.cwl/pv_maf_tag/output",
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"type": [
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"null",
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"File"
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],
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"outputBinding": {
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"glob": "${ \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}"
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}
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}
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],
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"label": "pv_maf_tag",
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"arguments": [
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"maf",
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"tag",
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"cmo_ch",
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{
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"position": 2,
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"prefix": "--output",
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"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}"
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}
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],
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"requirements": [
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{
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"class": "ResourceRequirement",
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"ramMin": 8000,
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"coresMin": 2
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},
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{
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"class": "DockerRequirement",
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"dockerPull": "ghcr.io/msk-access/postprocessing_variant_calls:chipvar_dev10"
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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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"http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center"
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}
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],
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"http://purl.org/dc/terms/creator": [
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"class": "http://xmlns.com/foaf/0.1/Organization",
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"class": "http://xmlns.com/foaf/0.1/Person",
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"http://xmlns.com/foaf/0.1/name": "Karthigayini Sivaprakasam"
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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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}
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],
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"class": "http://usefulinc.com/ns/doap#Version",
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"http://usefulinc.com/ns/doap#revision": "0.2.3"
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}
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]
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},
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{
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"class": "Workflow",
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"id": "#main",
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"label": "chipvar_processing",
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"inputs": [
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{
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"id": "#main/output_maf_name_filter",
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"type": [
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},
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],
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{
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"id": "#main/input_variant_annotated_maf",
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"https://www.sevenbridges.com/x": -1012.5234375,
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"https://www.sevenbridges.com/y": 20
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],
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"outputs": [
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{
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"id": "#main/output_maf_cmoch_filtered",
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"outputSource": [
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"#main/pv_maf_filter/output"
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"steps": [
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{
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"id": "#main/pv_maf_filter",
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"in": [
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{
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"id": "#main/pv_maf_filter/input_maf",
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"source": "#main/pv_maf_tag/output"
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"id": "#main/pv_maf_filter/output_maf_name",
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"id": "#main/pv_maf_filter/output"
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],
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"label": "pv_maf_filter",
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"id": "#main/pv_maf_tag",
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"in": [
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{
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"id": "#main/pv_maf_tag/input_maf",
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"source": "#main/input_variant_annotated_maf"
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},
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{
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"id": "#main/pv_maf_tag/output_maf_name",
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"source": "#main/output_maf_name_tag"
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}
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],
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"out": [
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"id": "#main/pv_maf_tag/output"
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}
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],
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"run": "#maf_tag_cmoch.cwl",
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"label": "pv_maf_tag",
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"https://www.sevenbridges.com/y": -80
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"cwlVersion": "v1.0",
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"$namespaces": {
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"sbg": "https://www.sevenbridges.com/"
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}
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}

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