@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: .
sld:type xsd:float , sld:null .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:in , , , , , , , ;
cwl:out , ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(runtime.outdir)/$(self.basename)"
] ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(runtime.outdir)/$(self.basename)"
] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:in , ;
cwl:out , , , , , ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"*.Germline.vcf" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"*.Germline.vcf" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
8 ] ;
sld:type cwl:File , sld:null .
sld:type cwl:File , sld:null .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:outputSource ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
sld:type xsd:float , sld:null .
cwl:default 9.9e-01 ;
cwl:inputBinding [ CommandLineBinding:position
7 ] ;
sld:type xsd:float , sld:null .
cwl:source .
cwl:source .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"*.Germline.hc.vcf" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"*.Germline.hc.vcf" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:in , ;
cwl:out , , , , , ;
cwl:run .
cwl:default 0 ;
cwl:inputBinding [ CommandLineBinding:position
4 ] ;
sld:type xsd:int , sld:null .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"output.indel.vcf" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
sld:type xsd:int , sld:null .
cwl:default 1e-01 ;
cwl:inputBinding [ CommandLineBinding:position
6 ] ;
sld:type xsd:float , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"*.LOH.hc.vcf" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"*.LOH.hc.vcf" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"*.Somatic.hc.vcf" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"*.Somatic.hc.vcf" ] ;
sld:type cwl:File .
cwl:source .
a cwl:Workflow ;
rdfs:label "varscan somatic workflow" ;
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:outputSource ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"output.snp.vcf" ] ;
sld:type cwl:File .
cwl:source .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , xsd:string .
cwl:default 8 ;
cwl:inputBinding [ CommandLineBinding:position
5 ] ;
sld:type xsd:int , sld:null .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--max-normal-freq"
] ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--max-normal-freq"
] ;
sld:type xsd:float , sld:null .
cwl:source .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"*.LOH.vcf" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"*.LOH.vcf" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "varscan v2.4.2 somatic" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "varscan_helper.sh" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/cle:v1.3.1"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 12000
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "#!/bin/bash\n\nset -o errexit\nset -o nounset\n\nif [ $# -lt 7 ]\nthen\n echo \"Usage: $0 [TUMOR_BAM] [NORMAL_BAM] [REFERENCE] [STRAND_FILTER] [MIN_COVERAGE] [MIN_VAR_FREQ] [P_VALUE] [roi_bed?]\"\n exit 1\nfi\n\nTUMOR_BAM=\"$1\"\nNORMAL_BAM=\"$2\"\nREFERENCE=\"$3\"\nSTRAND_FILTER=\"$4\"\nMIN_COVERAGE=\"$5\"\nMIN_VAR_FREQ=\"$6\"\nP_VALUE=\"$7\"\nOUTPUT=\"${HOME}/output\"\n\nif [ -z ${8+x} ]\nthen\n #run without ROI\n java -jar /opt/varscan/VarScan.jar somatic \\\n <(/opt/samtools/bin/samtools mpileup --no-baq -f \"$REFERENCE\" \"$NORMAL_BAM\" \"$TUMOR_BAM\") \\\n $OUTPUT \\\n --strand-filter $STRAND_FILTER \\\n --min-coverage $MIN_COVERAGE \\\n --min-var-freq $MIN_VAR_FREQ \\\n --p-value $P_VALUE \\\n --mpileup 1 \\\n --output-vcf\nelse\n ROI_BED=\"$8\"\n java -jar /opt/varscan/VarScan.jar somatic \\\n <(/opt/samtools/bin/samtools mpileup --no-baq -l \"$ROI_BED\" -f \"$REFERENCE\" \"$NORMAL_BAM\" \"$TUMOR_BAM\") \\\n $OUTPUT \\\n --strand-filter $STRAND_FILTER \\\n --min-coverage $MIN_COVERAGE \\\n --min-var-freq $MIN_VAR_FREQ \\\n --p-value $P_VALUE \\\n --mpileup 1 \\\n --output-vcf\nfi\n" ;
cwl:entryname "varscan_helper.sh"
]
] .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
sld:type xsd:int , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"*.Somatic.vcf" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"*.Somatic.vcf" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , xsd:string .
cwl:outputSource ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
sld:type xsd:float , sld:null .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "varscan v2.4.2 processSomatic" ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( "cp" "$(inputs.variants.path)" "$(runtime.outdir)/$(inputs.variants.basename)"
[ CommandLineBinding:shellQuote false ;
cwl:valueFrom " && "
]
"java" "-jar" "/opt/varscan/VarScan.jar" "processSomatic"
) ;
cwl:arguments ( "cp" "$(inputs.variants.path)" "$(runtime.outdir)/$(inputs.variants.basename)"
[ CommandLineBinding:shellQuote false ;
cwl:valueFrom " && "
]
"java" "-jar" "/opt/varscan/VarScan.jar" "processSomatic"
) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , ;
cwl:outputs , , , , , ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/cle:v1.3.1"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/cle:v1.3.1"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] .
cwl:source .