@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:source .
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
a cwl:Workflow ;
rdfs:label "exome 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:SubworkflowFeatureRequirement ] .
rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ;
sld:type xsd:string .
cwl:source .
sld:type cwl:File .
sld:type [ sld:items [ sld:items xsd:string ;
sld:type sld:array
] ;
sld:type sld:array
] .
cwl:inputBinding [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(self.basename)"
] ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(self.basename)"
] ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 7 ;
cwl:valueFrom "${\n if (inputs.custom_clinvar_vcf) {\n return [\"--custom\", inputs.custom_clinvar_vcf.path + \",clinvar,vcf,exact,0,CLINSIGN,PHENOTYPE,SCORE,RCVACC,TESTEDINGTR,PHENOTYPELIST,NUMSUBMIT,GUIDELINES\"]\n\n }\n else {\n return []\n }\n}\n"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-R"
] ;
sld:type xsd:string .
cwl:default true .
cwl:inputBinding [ CommandLineBinding:position
9 ] ;
sld:type [ cwl:inputBinding [ CommandLineBinding:prefix
"--plugin" ] ;
sld:items xsd:string ;
sld:type sld:array
] .
cwl:in , , , ;
cwl:out ;
cwl:run .
cwl:source .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.file.basename).gz" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.file.basename).gz" ] ;
sld:type cwl:File .
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
cwl:source .
rdfs:comment "genome assembly to use in vep. Examples: 'GRCh38' or 'GRCm38'" ;
cwl:inputBinding [ CommandLineBinding:position 11 ;
CommandLineBinding:prefix "--assembly"
] ;
sld:type xsd:string .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "--dir"
] ;
sld:type xsd:string .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 8 ;
CommandLineBinding:prefix "--fasta"
] ;
sld:type xsd:string , sld:null .
a cwl:Workflow ;
rdfs:label "scatter GATK HaplotypeCaller over intervals" ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ;
sld:type xsd:string .
cwl:in ;
cwl:out ;
cwl:run .
cwl:default "output.g.vcf.gz" ;
cwl:inputBinding [ CommandLineBinding:position 8 ;
CommandLineBinding:prefix "-o"
] ;
sld:type xsd:string .
a cwl:CommandLineTool ;
rdfs:label "add VEP annotation to report" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-o"
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.prefix).annotated.tsv" ]
) ;
cwl:baseCommand ( "vep-annotation-reporter" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "griffithlab/vatools:3.1.0"
] .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:source .
rdfs:comment "ensembl species - Must be present in the cache directory. Examples: 'homo_sapiens' or 'mus_musculus'" ;
cwl:inputBinding [ CommandLineBinding:position 13 ;
CommandLineBinding:prefix "--species"
] ;
sld:type xsd:string .
sld:type xsd:string .
cwl:source .
cwl:source .
cwl:in , , , , , , , , , , ;
cwl:out , ;
cwl:run .
cwl:default "ID" , "ALT" , "CHROM" , "POS" , "REF" ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-R"
] ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--variant"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"genotype.vcf.gz" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:in , , , , , , , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 6 ;
cwl:valueFrom "${\n if (inputs.custom_gnomad_vcf) {\n return ['--check_existing', '--custom', inputs.custom_gnomad_vcf.path + ',gnomADe,vcf,exact,0,AF,AF_AFR,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,AF_NFE,AF_OTH,AF_SAS']\n }\n else {\n return []\n }\n}\n"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
cwl:in , , , ;
cwl:out ;
cwl:run .
cwl:source .
cwl:source .
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 ;
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 6000 ;
ResourceRequirement:tmpdirMin 25000
] .
cwl:source .
cwl:in , , , ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-I"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:valueFrom "${ if (inputs.intervals.length == 1 && inputs.intervals[0].match(/^[0-9A-Za-z]+$/)) { return inputs.intervals[0] + \".g.vcf.gz\"; } else { return \"output.g.vcf.gz\"; } }" .
cwl:outputBinding [ CommandOutputBinding:glob
"annotated.vcf" ] ;
sld:type cwl:File .
cwl:source .
sld:type cwl:File , sld:null .
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 ;
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:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] ;
cwl:stdout "$(inputs.file.basename).gz" .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.vcf.basename)" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.vcf.basename)" ] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type xsd:string , sld:null .
cwl:source .
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
cwl:in ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-i"
] ;
sld:type cwl:File .
cwl:default "variants" ;
sld:type xsd:string , sld:null .
sld:type xsd:string .
cwl:default "Wildtype" , "Downstream" ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:default true ;
cwl:inputBinding [ CommandLineBinding:position 10 ;
CommandLineBinding:prefix "--everything"
] ;
sld:type xsd:boolean , sld:null .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.prefix).annotated.tsv" ] ;
sld:type cwl:File .
cwl:source .
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-i"
] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .