@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:in , ;
cwl:out ;
cwl:run .
cwl:source .
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "Read-backed phasing" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-L"
[ cwl:valueFrom "$(inputs.vcf)" ]
"-o"
[ cwl:valueFrom "$(runtime.outdir)/phased.vcf" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "ReadBackedPhasing" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 9000 ;
ResourceRequirement:tmpdirMin 25000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0"
] .
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "-V"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "Sort VCF" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "O="
[ cwl:valueFrom "$(runtime.outdir)/sorted.vcf" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/opt/picard/picard.jar" "SortVcf" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 18000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1"
] .
cwl:outputBinding [ CommandOutputBinding:glob
"phased.vcf" ] ;
sld:type cwl:File .
cwl:source .
sld:type cwl:File .
sld:type xsd:string .
a cwl:CommandLineTool ;
rdfs:label "Combine germline and somatic vcf for pVACseq phasing" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "--assumeIdenticalSamples" "-o"
[ cwl:valueFrom "$(runtime.outdir)/combined_somatic_plus_germline.vcf" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "CombineVariants" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 9000 ;
ResourceRequirement:tmpdirMin 25000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0"
] .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
a cwl:Workflow ;
rdfs:label "bgzip and index VCF" ;
ns1:original_cwlVersion "v1.2" ;
Workflow:steps , ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs ;
cwl:outputs .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:outputSource ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"I=" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-R"
] ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-R"
] ;
sld:type xsd:string .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.file.basename).gz" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.file.basename).gz" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "bgzip VCF" ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( "-c" ) ;
cwl:arguments ( "-c" ) ;
cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ;
cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0"
] ;
cwl:stdout "$(inputs.file.basename).gz" .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-V"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"sorted.vcf" ] ;
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
cwl:source .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-I"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:in , , ;
cwl:out ;
cwl:run .
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "-V"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"SEQUENCE_DICTIONARY=" ] ;
sld:type cwl:File , sld:null .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.vcf.basename)" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.vcf.basename)" ] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(self.basename)"
] ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(self.basename)"
] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"combined_somatic_plus_germline.vcf" ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:source .
a cwl:Workflow ;
rdfs:label "phase VCF" ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , , , , ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] .
a cwl:CommandLineTool ;
rdfs:label "vcf index" ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
[ CommandLineBinding:shellQuote false ;
cwl:valueFrom " && "
]
"/usr/bin/tabix" "-p" "vcf"
) ;
cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
[ CommandLineBinding:shellQuote false ;
cwl:valueFrom " && "
]
"/usr/bin/tabix" "-p" "vcf"
) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
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/samtools-cwl:1.0.0"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0"
] .
cwl:in ;
cwl:out ;
cwl:run .