@prefix LoadListingRequirement: .
@prefix SchemaDefRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix ScatterMethod: .
@prefix cwl: .
@prefix ResourceRequirement: .
@prefix ExpressionTool: .
a cwl:Workflow ;
rdfs:label "wgs alignment with qc" ;
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:SubworkflowFeatureRequirement ] ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types
] .
cwl:outputSource ;
sld:type cwl:File , sld:null .
a cwl:CommandLineTool ;
rdfs:label "Ensembl Variant Effect Predictor" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "--format" "vcf" "--vcf" "--fork" "4" "--plugin" "Downstream" "--plugin" "Wildtype" "--term" "SO" "--transcript_version" "--offline" "--cache" "--everything" "-o"
[ cwl:valueFrom "$(runtime.outdir)/annotated.vcf" ]
) ;
cwl:baseCommand ( "/usr/bin/perl" "-I" "/opt/lib/perl/VEP/Plugins" "/usr/bin/variant_effect_predictor.pl" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/vep_helper-cwl:1.0.0"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 4 ;
ResourceRequirement:ramMin 64000 ;
ResourceRequirement:tmpdirMin 25000
] .
cwl:in ;
cwl:out ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.vcf.basename)" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.vcf.basename)" ] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:outputSource ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.bam.nameroot).VerifyBamId.selfSM" ] ;
sld:type cwl:File .
sld:type xsd:boolean , sld:null .
sld:type xsd:boolean , sld:null .
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
sld:type xsd:int , sld:null .
sld:type xsd:string .
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).$(inputs.output_prefix)-HsMetrics.txt" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , , , , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 52000
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 52000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1"
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 52000
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
a cwl:CommandLineTool ;
rdfs:label "collect gc bias metrics" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "O="
[ cwl:valueFrom "$(runtime.outdir)/GcBiasMetrics.txt" ]
"CHART="
[ cwl:valueFrom "$(runtime.outdir)/GcBiasMetricsChart.pdf" ]
"S="
[ cwl:valueFrom "$(runtime.outdir)/GcBiasMetricsSummary.txt" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectGcBiasMetrics" ) ;
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 18000
] .
sld:type xsd:int , sld:null .
cwl:source .
cwl:outputSource ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 10 ;
CommandLineBinding:prefix "--drop-low-coverage"
] ;
sld:type xsd:boolean , sld:null .
cwl:in , , , , , , , , , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) ;
cwl:scatterMethod ScatterMethod:dotproduct .
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "--dbsnp"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
cwl:in , , , , , ;
cwl:out ;
cwl:run .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
cwl:source .
rdfs:label "a file with a label" ;
sld:fields , ;
sld:type sld:record .
cwl:outputSource ;
sld:type cwl:File , sld:null .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.cohort_name)-smoove.genotyped.vcf.gz" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:default "Final.bam" ;
sld:type xsd:string , sld:null .
cwl:source .
a cwl:Workflow ;
rdfs:label "exome alignment and germline variant detection" ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , , , , , , , , ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , , , , , , ;
cwl:outputs , , , , ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] .
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File , sld:null .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
a cwl:Workflow ;
rdfs:label "scatter GATK HaplotypeCaller over intervals" ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:in , , , , , , ;
cwl:out , ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:prefix
"R=" ] ;
sld:type xsd:string .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"${\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 .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run .
cwl:in , , , , ;
cwl:out , ,