@prefix LoadListingRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix cwl: .
@prefix ResourceRequirement: .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.tumor_bam.nameroot)-scatter.pdf" ] ;
sld:type cwl:File , sld:null .
cwl:in , , , , ;
cwl:out ;
cwl:run .
sld:type xsd:boolean , sld:null .
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.tumor_bam.nameroot).antitargetcoverage.cnn" ] ;
sld:type cwl:File .
sld:type xsd:boolean , sld:null .
cwl:outputSource ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var glob_base = \".targetcoverage.cnn\";\n if (inputs.normal_bam) {\n glob_base = inputs.normal_bam.nameroot + glob_base;\n }\n return glob_base;\n}\n" ] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "--targets"
] ;
sld:type cwl:File , sld:null .
cwl:outputSource ;
sld:type cwl:File , sld:null .
cwl:outputSource ;
sld:type cwl:File , sld:null .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "--fasta"
] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--normal"
] ;
sld:type cwl:File , sld:null .
sld:type sld:null ;
sld:type [ sld:symbols , , , ;
sld:type sld:enum
] .
a cwl:CommandLineTool ;
rdfs:label "Convert default cnvkit .cns output to standard vcf format" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position -1 ;
CommandLineBinding:prefix "-y" ;
cwl:valueFrom "$(inputs.male_reference)"
]
"-o" "adjusted.tumor.cns"
[ CommandLineBinding:shellQuote false ;
cwl:valueFrom "&&"
]
"/usr/bin/python" "/usr/local/bin/cnvkit.py" "export" "vcf" "adjusted.tumor.cns"
) ;
cwl:baseCommand ( "/usr/bin/python" "/usr/local/bin/cnvkit.py" "call" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 8000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "etal/cnvkit:0.9.5"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:inputBinding [ CommandLineBinding:prefix
"-r" ] ;
sld:type cwl:File , sld:null .
cwl:default "hybrid" ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "--method"
] ;
sld:type xsd:string , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var glob_base = \".antitargetcoverage.cnn\";\n if (inputs.normal_bam) {\n glob_base = inputs.normal_bam.nameroot + glob_base;\n }\n return glob_base;\n}\n" ] ;
sld:type cwl:File , sld:null .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "/usr/bin/python" "/usr/local/bin/cnvkit.py" "batch" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , , , , , ;
cwl:outputs , , , , , , , , , , ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "etal/cnvkit:0.9.5"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:ramMin 4000 ;
ResourceRequirement:tmpdirMin 10000
] .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.tumor_bam.nameroot).cns" ] ;
sld:type cwl:File .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"reference.cnn" ] ;
sld:type cwl:File , sld:null .
rdfs:comment "method for filtering/merging neighboring copy number segments" ;
cwl:inputBinding [ CommandLineBinding:position -3 ;
CommandLineBinding:prefix "--filter"
] ;
sld:type sld:null ;
sld:type [ sld:symbols , , , ;
sld:type sld:enum
] .
sld:type xsd:string , sld:null .
cwl:source ;
cwl:valueFrom "${ \n if(inputs.output_name) {\n return inputs.output_name;\n } \n else {\n return inputs.tumor_bam.nameroot + \".cnvkit.vcf\"\n } \n}\n" .
cwl:source .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.tumor_bam.nameroot)-diagram.pdf" ] ;
sld:type cwl:File , sld:null .
sld:type xsd:boolean , sld:null .
a cwl:Workflow ;
rdfs:label "Subworkflow that runs cnvkit in single sample mode and returns a vcf file" ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , , , ;
cwl:outputs , , , , , , ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_name)" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--cnr"
] ;
sld:type cwl:File , sld:null .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var glob_base = \".target.bed\";\n if (inputs.bait_intervals) {\n glob_base = inputs.bait_intervals.nameroot + glob_base;\n }\n return glob_base;\n}\n" ] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:position 7 ;
CommandLineBinding:prefix "--diagram"
] ;
sld:type xsd:boolean , sld:null .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "--access"
] ;
sld:type cwl:File , sld:null .
cwl:in , , , , , , ;
cwl:out , , , , , ;
cwl:run .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.tumor_bam.nameroot).targetcoverage.cnn" ] ;
sld:type cwl:File .
sld:type xsd:boolean , sld:null .
sld:type cwl:File .
cwl:default "hybrid" ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position
-2 ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"-y" ] ;
sld:type xsd:boolean , sld:null .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"${ \n var glob_base = \".antitarget.bed\";\n if (inputs.bait_intervals) {\n glob_base = inputs.bait_intervals.nameroot + glob_base;\n } \n return glob_base;\n} \n" ] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:position 10 ;
CommandLineBinding:prefix "--drop-low-coverage"
] ;
sld:type xsd:boolean , sld:null .
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-y"
] ;
sld:type xsd:boolean , sld:null .
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "-o"
] ;
sld:type xsd:string .
cwl:outputSource ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 8 ;
CommandLineBinding:prefix "--scatter"
] ;
sld:type xsd:boolean , sld:null .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.tumor_bam.nameroot).cnr" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .