@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: .
cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ;
cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n"
] ;
cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ;
cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n"
] ;
cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ;
cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n"
] ;
sld:type xsd:boolean , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"INPUT=" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"METRIC_ACCUMULATION_LEVEL=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"METRIC_ACCUMULATION_LEVEL=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"METRIC_ACCUMULATION_LEVEL=" ] ;
sld:type xsd:string .
cwl:source .
cwl:source .
sld:type xsd:string , sld:null .
cwl:source .
cwl:source ;
cwl:valueFrom "$(self.file)" .
cwl:source .
sld:type , sld:null .
cwl:source .
cwl:source .
rdfs:comment "Minimum overlap for removal without pair overlap." ;
sld:type xsd:int .
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 .
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 ;
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/gatk:4.1.8.1"
] .
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
sld:type xsd:int , sld:null .
cwl:source .
cwl:source .
cwl:source .
a cwl:Workflow ;
rdfs:label "HS Metrics 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:requirements [ a cwl:ScatterFeatureRequirement ] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types
] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:source .
rdfs:comment "Minimum base quality for a base to contribute coverage. (N bases are considered to have negative infinite quality and will be excluded regardless of this value.)" ;
cwl:inputBinding [ CommandLineBinding:prefix
"MINIMUM_BASE_QUALITY=" ] ;
sld:type xsd:int , sld:null .
cwl:source ;
cwl:valueFrom "target-$(self.label)" .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type cwl:File .
sld:type xsd:int , sld:null .
cwl:in , , , , , , ;
cwl:out , , , , ;
cwl:run .
a cwl:Workflow ;
rdfs:comment "Some workflow engines won't stage files in our nested structure, so parse it out here" ;
rdfs:label "adapter for sequence_align_and_tag" ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types ,
] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:in ;
cwl:out ;
cwl:run .
cwl:source .
cwl:outputSource ;
sld:type cwl:File .
sld:type [ sld:items ;
sld:type sld:array
] .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:default "final" ;
sld:type xsd:string , sld:null .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
cwl:default true .
rdfs:comment "filters to apply to reads before analysis" ;
cwl:inputBinding [ CommandLineBinding:position 10 ;
CommandLineBinding:prefix "--read_filter"
] ;
sld:type xsd:string , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_name).bam" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:source .
cwl:outputSource ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"-g" ] ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"bqsr.table" ] ;
sld:type cwl:File .
cwl:default "false" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-s"
] ;
sld:type xsd:boolean , sld:null .
cwl:source .
cwl:source .
cwl:source .
cwl:default 1 ;
cwl:inputBinding [ CommandLineBinding:prefix
"MINIMUM_BASE_QUALITY=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"MINIMUM_BASE_QUALITY=" ] ;
cwl:inputBinding [ CommandLineBinding:prefix
"MINIMUM_BASE_QUALITY=" ] ;
sld:type xsd:int , sld:null .
cwl:outputSource ;
sld:type cwl:File .
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , xsd:string .
cwl:default "chr10" , "chr15" , "chr16" , "chr11" , "chr6" , "chr1" , "chr17" , "chr7" , "chr12" , "chr2" , "chr3" , "chr19" , "chr18" , "chr8" , "chr13" , "chr4" , "chr20" , "chr9" , "chr14" , "chr5" , "chr21" , "chr22" ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type [ cwl:inputBinding [ CommandLineBinding:prefix
"-L" ] ;
sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
sld:type xsd:int , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.sample_name).GcBiasMetrics.txt" ] ;
sld:type cwl:File .
cwl:source .
sld:type cwl:File .
sld:type [ sld:symbols , , ;
sld:type sld:enum
] .
a cwl:Workflow ;
rdfs:label "wgs alignment and germline variant detection" ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , , , , ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , , , , , , , , , , , , , ;
cwl:outputs , , , , , , , , , , , , , , , , , ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types , ,
] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] .
a cwl:Workflow ;
rdfs:label "Raw sequence data to BQSR" ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , , , , , , ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types ,
] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] .
a cwl:CommandLineTool ;
rdfs:label "verify BAM ID" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "--out"
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).VerifyBamId" ]
) ;
cwl:baseCommand ( "/usr/local/bin/verifyBamID" ) ;
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 4000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/verify_bam_id-cwl:1.1.3"
] .
cwl:inputBinding [ CommandLineBinding:prefix
"-1" ] ;
sld:type cwl:File , sld:null .
sld:type cwl:File .