@prefix LoadListingRequirement: .
@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: .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type xsd:int , sld:null .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type xsd:int , sld:null .
cwl:source ;
cwl:valueFrom "$(self.downsample_ratio)" .
cwl:inputBinding [ CommandLineBinding:position
4 ] ;
sld:type [ cwl:inputBinding [ CommandLineBinding:prefix
"-GQB" ] ;
sld:items xsd:string ;
sld:type sld:array
] .
cwl:inputBinding [ CommandLineBinding:prefix
"R=" ] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , xsd:string .
cwl:in , , , , , , , , , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) ;
cwl:scatterMethod ScatterMethod:dotproduct .
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
sld:type xsd:string , sld:null .
sld:fields , , ;
sld:type sld:record .
sld:type cwl:File .
cwl:source .
cwl:source .
sld:type sld:null ;
sld:type [ sld:symbols , , ;
sld:type sld:enum
] .
cwl:inputBinding [ CommandLineBinding:prefix
"I=" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
sld:type [ sld:symbols , , ;
sld:type sld:enum
] .
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , xsd:string .
sld:type xsd:int .
cwl:source .
rdfs:comment "the downsample ratio to use when reprocessing this CRAM" ;
sld:type xsd:float .
sld:type xsd:int .
sld:type xsd:int , sld:null .
rdfs:comment "filters to apply to reads before analysis" ;
cwl:inputBinding [ CommandLineBinding:position 10 ;
CommandLineBinding:prefix "--read_filter"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "the downsample ratio to use when reprocessing this CRAM" ;
sld:type xsd:float .
rdfs:comment "an optional string to prepend to the output filename" ;
sld:type xsd:string , sld:null .
cwl:default "output.g.vcf.gz" ;
cwl:inputBinding [ CommandLineBinding:position 11 ;
CommandLineBinding:prefix "-O"
] ;
sld:type xsd:string .
cwl:source .
cwl:source .
sld:fields , , ;
sld:type sld:record .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type xsd:string .
sld:type [ sld:items ;
sld:type sld:array
] .
cwl:inputBinding [ CommandLineBinding:position
5 ] ;
sld:type [ cwl:inputBinding [ CommandLineBinding:prefix
"-L" ] ;
sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
sld:type xsd:string , sld:null .
cwl:source .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "collect WGS metrics" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "O="
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.sample_name).WgsMetrics.txt" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectWgsMetrics" ) ;
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 18000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "broadinstitute/picard:2.23.6"
] .
cwl:inputBinding [ CommandLineBinding:prefix "--STRATEGY=" ;
CommandLineBinding:separate false
] ;
sld:type sld:null ;
sld:type [ sld:symbols , , ;
sld:type sld:enum
] .
cwl:in , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) ;
cwl:scatterMethod ScatterMethod:dotproduct .
sld:type xsd:int .
sld:type xsd:int , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"INTERVALS=" ] ;
sld:type cwl:File , sld:null .
rdfs:comment "arrays of intervals to use in each individual run of the haplotypecaller" ;
sld:type [ sld:items [ sld:items xsd:string ;
sld:type sld:array
] ;
sld:type sld:array
] .
cwl:source .
a cwl:Workflow ;
rdfs:label "Gathered Downsample and HaplotypeCaller" ;
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:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] .
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "--dbsnp"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
sld:type [ sld:items ;
sld:type sld:array
] .
cwl:source .
cwl:in , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) ;
cwl:scatterMethod ScatterMethod:dotproduct .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-R"
] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , xsd:string .
sld:type [ sld:items [ sld:items xsd:string ;
sld:type sld:array
] ;
sld:type sld:array
] .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_file_name)" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
sld:type xsd:int , sld:null .
sld:type [ sld:symbols , , ;
sld:type sld:enum
] .
a cwl:CommandLineTool ;
rdfs:label "GATK HaplotypeCaller" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx16g" "HaplotypeCaller" ) ;
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 "broadinstitute/gatk:4.1.8.1"
] .
rdfs:comment "number of chromosomes per sample" ;
cwl:inputBinding [ CommandLineBinding:position 9 ;
CommandLineBinding:prefix "-ploidy"
] ;
sld:type xsd:int , sld:null .
cwl:source .
sld:type xsd:string , sld:null .
rdfs:comment "contamination score to pass to HaplotypeCaller" ;
sld:type xsd:float .
a cwl:Workflow ;
rdfs:label "Downsample and HaplotypeCaller" ;
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:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source ;
cwl:valueFrom "$(self.cram)" .
cwl:source .
sld:type cwl:File .
cwl:in , , , , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) ;
cwl:scatterMethod ScatterMethod:dotproduct .
cwl:inputBinding [ CommandLineBinding:prefix "--REFERENCE_SEQUENCE=" ;
CommandLineBinding:separate false
] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , xsd:string .
rdfs:comment "The reference that was used for the already-completed alignments" ;
sld:type cwl:File , xsd:string .
sld:type xsd:string , sld:null .
cwl:in , , , , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) ;
cwl:scatterMethod ScatterMethod:dotproduct .
rdfs:comment "The reference that was used for the already-completed alignments" ;
sld:type cwl:File , xsd:string .
cwl:source .
cwl:source .
cwl:source ;
cwl:valueFrom "$(self.nameroot)" .
cwl:source .
cwl:source .
rdfs:comment "maximum number of alternate alleles to genotype" ;
cwl:inputBinding [ CommandLineBinding:position 8 ;
CommandLineBinding:prefix "--max_alternate_alleles"
] ;
sld:type xsd:int , sld:null .
cwl:source ;
cwl:valueFrom "${ var prefix = self !== null ? self : \"\"; if (inputs.intervals.length == 1 && inputs.intervals[0].match(/^[0-9A-Za-z]+$/)) { return prefix + inputs.intervals[0] + \".g.vcf.gz\"; } else { return prefix + \"output.g.vcf.gz\"; } }" .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 7 ;
CommandLineBinding:prefix "-contamination"
] ;
sld:type xsd:string , sld:null .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
rdfs:comment "Minimum mapping quality for a read to contribute coverage." ;
cwl:inputBinding [ CommandLineBinding:prefix
"MINIMUM_MAPPING_QUALITY=" ] ;
sld:type xsd:int , sld:null .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix "--PROBABILITY=" ;
CommandLineBinding:separate false
] ;
sld:type xsd:float .
cwl:source .
cwl:source ;
cwl:valueFrom "$(self.nameroot + \".downsampled.\")" .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.sam.nameroot).bam" ] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .