@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:secondaryFiles [] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "vcf merge" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "--allow-overlaps" "--remove-duplicates" "--output-type" "z" "-o"
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.merged_vcf_basename).vcf.gz" ]
) ;
cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "concat" ) ;
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 4000
] .
cwl:outputBinding [ CommandOutputBinding:glob
"panel_of_normals.vcf.gz" ] ;
sld:type cwl:File .
cwl:default "fpfilter" ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:default "select_variants" ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "--dbsnp"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position 7 ;
CommandLineBinding:prefix "--artifact_detection_mode"
] ;
sld:type xsd:boolean , sld:null .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "SCATTER_COUNT=" ;
CommandLineBinding:separate false
] ;
sld:type xsd:int .
cwl:source .
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
cwl:secondaryFiles [] ;
sld:type [ cwl:inputBinding [ CommandLineBinding:prefix
"-V" ] ;
sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"decomposed.vcf.gz" ] ;
sld:type cwl:File .
sld:type xsd:string .
cwl:source .
a cwl:Workflow ;
rdfs:label "mutect parallel workflow" ;
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:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] .
cwl:in ;
cwl:out ;
cwl:run .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-R"
] ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_vcf_basename).vcf" ] ;
sld:type cwl:File .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"mutect.vcf.gz" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "run vt decompose" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-s" "-o"
[ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ]
) ;
cwl:baseCommand ( "vt" "decompose" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] .
sld:type xsd:boolean .
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: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 ;
NetworkAccess:networkAccess true
] ;
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:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
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:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0"
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] .
cwl:source .
cwl:valueFrom "mutect" .
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
cwl:source .
cwl:in , , , , , , , , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) .
cwl:source .
cwl:source .
cwl:source .
cwl:source .
cwl:source .
sld:type xsd:float , sld:null .
cwl:source .
cwl:source .
cwl:source .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--bam-file"
] ;
sld:type cwl:File .
cwl:source .
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "-I:normal"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
cwl:secondaryFiles [] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
rdfs:label "Normalize variants" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-o"
[ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "LeftAlignAndTrimVariants" ) ;
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/gatk-cwl:3.6.0"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 9000
] .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
sld:type xsd:string .
sld:type xsd:int , sld:null .
a cwl:Workflow ;
rdfs:label "mutect panel-of-normals workflow" ;
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:ScatterFeatureRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] .
cwl:source ;
cwl:valueFrom "$(self)_filtered" .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--reference"
] ;
sld:type xsd:string .
cwl:in ;
cwl:out ;
cwl:run .
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
cwl:default "merged" ;
sld:type xsd:string , sld:null .
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 10 ;
CommandLineBinding:prefix "--max_alt_allele_in_normal_fraction"
] ;
sld:type xsd:float , sld:null .
a cwl:CommandLineTool ;
rdfs:label "SelectVariants (GATK 3.6)" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-o"
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 6000 ;
ResourceRequirement:tmpdirMin 25000
] .
cwl:source .
cwl:default 5e-02 ;
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "--min-var-freq"
] ;
sld:type xsd:float , sld:null .
cwl:default true .
sld:type xsd:float , sld:null .
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(self.basename)"
] ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(self.basename)"
] ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(self.basename)"
] ;
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--variant"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ cwl:valueFrom "OUTPUT=$(runtime.outdir)" ]
) ;
cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/split_interval_list_helper.pl" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/cle:v1.3.1"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 6000
] .
sld:type xsd:string .
a cwl:CommandLineTool ;
rdfs:label "CombineVariants for Panel of Normals" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-minN" "2" "--setKey" "null" "--filteredAreUncalled" "--filteredrecordsmergetype" "KEEP_IF_ANY_UNFILTERED" "-o"
[ cwl:valueFrom "$(runtime.outdir)/panel_of_normals.vcf.gz" ]
) ;
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/cle:v1.3.1"
] .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:in , , , , , , , , , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) .
cwl:source .
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-I:tumor"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_vcf_basename).vcf.gz" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-L"
] ;
sld:type cwl:File , sld:null .
a cwl:CommandLineTool ;
rdfs:label "False Positive filter" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output"
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ]
) ;
cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ;
cwl:cwlVersion