@prefix SchemaDefRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
@prefix rdf: .
@prefix ScatterMethod: .
@prefix cwl: .
@prefix ResourceRequirement: .
cwl:source ;
cwl:valueFrom "$(self.file)" .
cwl:inputBinding [ CommandLineBinding:prefix
"METRIC_ACCUMULATION_LEVEL=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"METRIC_ACCUMULATION_LEVEL=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"METRIC_ACCUMULATION_LEVEL=" ] ;
sld:type xsd:string .
sld:type [ sld:items ;
sld:type sld:array
] .
cwl:source ;
cwl:valueFrom "$(self.file)" .
cwl:source ;
cwl:valueFrom "$(self.file)" .
sld:type xsd:string .
cwl:source .
a cwl:Workflow ;
rdfs:label "HS Metrics workflow" ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , , ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:inputs , , , , , , ;
cwl:outputs , , , , ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types
] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ;
sld:type cwl:File , sld:null .
cwl:in , , , , , , , , , ;
cwl:out , ;
cwl:run ;
cwl:scatter ( ) ;
cwl:scatterMethod ScatterMethod:dotproduct .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:inputBinding [ CommandLineBinding:prefix
"TARGET_INTERVALS=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"TARGET_INTERVALS=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"TARGET_INTERVALS=" ] ;
sld:type cwl:File .
cwl:source ;
cwl:valueFrom "$(self.file)" .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"BAIT_INTERVALS=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"BAIT_INTERVALS=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"BAIT_INTERVALS=" ] ;
sld:type cwl:File .
cwl:default false .
rdfs:label "a file with a label" ;
sld:fields , ;
sld:type sld:record .
cwl:in , , , , , , , , , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) ;
cwl:scatterMethod ScatterMethod:dotproduct .
cwl:source ;
cwl:valueFrom "base-$(self.label)" .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ;
sld:type cwl:File , sld:null .
cwl:default true .
cwl:default false .
cwl:in , , , , , , , , , ;
cwl:out , ;
cwl:run ;
cwl:scatter ( ) ;
cwl:scatterMethod ScatterMethod:dotproduct .
cwl:default true .
cwl:default false .
sld:type cwl:File .
cwl:default 1 ;
cwl:inputBinding [ CommandLineBinding:prefix
"MINIMUM_BASE_QUALITY=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"MINIMUM_BASE_QUALITY=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"MINIMUM_BASE_QUALITY=" ] ;
sld:type xsd:int , sld:null .
cwl:source .
cwl:source .
cwl:valueFrom "ALL_READS" .
sld:type xsd:int , sld:null .
cwl:source .
cwl:source ;
cwl:valueFrom "$(self.file)" .
cwl:source .
cwl:source .
sld:type [ sld:items ;
sld:type sld:array
] .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source ;
cwl:valueFrom "summary-$(self.label)" .
cwl:source ;
cwl:valueFrom "$(self.file)" .
cwl:inputBinding [ CommandLineBinding:prefix
"R=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"R=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"R=" ] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , xsd:string .
cwl:source ;
cwl:valueFrom "target-$(self.label)" .
sld:type [ sld:items ;
sld:type sld:array
] .
cwl:default 1 ;
cwl:inputBinding [ CommandLineBinding:prefix
"MINIMUM_MAPPING_QUALITY=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"MINIMUM_MAPPING_QUALITY=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"MINIMUM_MAPPING_QUALITY=" ] ;
sld:type xsd:int , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"I=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"I=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"I=" ] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:default "out" ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:source .
cwl:valueFrom "ALL_READS" .
cwl:source .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
rdfs:label "collect HS metrics" ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( "O="
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ]
) ;
cwl:arguments ( "O="
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ]
) ;
cwl:arguments ( "O="
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:inputs , , , , , , , , , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 52000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "broadinstitute/picard:2.23.6"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 52000
] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "broadinstitute/picard:2.23.6"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "broadinstitute/picard:2.23.6"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 52000
] .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ;
cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n"
] ;
cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ;
cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n"
] ;
cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ;
cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n"
] ;
sld:type xsd:boolean , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ;
cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n"
] ;
cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ;
cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n"
] ;
cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ;
cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n"
] ;
sld:type xsd:boolean , sld:null .
cwl:default false .
cwl:secondaryFiles [] ;
sld:type cwl:File .
sld:type xsd:int , sld:null .
cwl:valueFrom "ALL_READS" .
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , xsd:string .