@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 cwl: .
@prefix ResourceRequirement: .
cwl:source .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position 7 ;
CommandLineBinding:prefix "--fasta"
] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-D"
] ;
sld:type cwl:File , xsd:string , sld:null .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
cwl:in , ;
cwl:out ;
cwl:run .
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 .
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-i"
] ;
sld:type cwl:File .
cwl:default "flag_pick" ;
cwl:inputBinding [ CommandLineBinding:position 7 ;
CommandLineBinding:prefix "--" ;
CommandLineBinding:separate false
] ;
sld:type sld:null ;
sld:type [ sld:symbols , , , , , , ;
sld:type sld:enum
] .
sld:type xsd:string , sld:null .
cwl:in ;
cwl:out ;
cwl:run .
a cwl:CommandLineTool ;
rdfs:label "Ensembl Variant Effect Predictor" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "--format" "vcf" "--vcf" "--fork" "4" "--term" "SO" "--transcript_version" "--offline" "--cache" "--symbol" "-o"
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.vcf.nameroot)_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:SchemaDefRequirement ;
SchemaDefRequirement:types
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 4 ;
ResourceRequirement:ramMin 64000 ;
ResourceRequirement:tmpdirMin 25000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/vep_helper-cwl:vep_101.0_v1"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type [ cwl:inputBinding [ CommandLineBinding:prefix
"-I" ] ;
sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:source ;
cwl:valueFrom "${\n if(self){\n for(var i=0; i
cwl:in , , , ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "--exclude-filtered"
] ;
sld:type xsd:boolean , sld:null .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--variant"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
rdfs:comment "custom type, check types directory for input format" ;
sld:type [ sld:items ;
sld:type sld:array
] .
cwl:source .
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , xsd:string .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
a cwl:CommandLineTool ;
rdfs:comment "Renames a file by staging and then `mv`ing it. A workaround for workflow engines that don't support rename.cwl. If running in cwltool, use the other one instead." ;
rdfs:label "Staged Renamer" ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( "$(inputs.original.basename)" "$(inputs.name)" ) ;
cwl:arguments ( "$(inputs.original.basename)" "$(inputs.name)" ) ;
cwl:arguments ( "$(inputs.original.basename)" "$(inputs.name)" ) ;
cwl:baseCommand ( "/bin/mv" ) ;
cwl:baseCommand ( "/bin/mv" ) ;
cwl:baseCommand ( "/bin/mv" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "$(inputs.original)"
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ubuntu:bionic"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:ramMin 4000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ubuntu:bionic"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:ramMin 4000
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:ramMin 4000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ubuntu:bionic"
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "$(inputs.original)"
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "$(inputs.original)"
] .
cwl:outputSource ;
sld:type cwl:File .
sld:type xsd:float .
cwl:inputBinding [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(self.basename)"
] ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(self.basename)"
] ;
sld:type cwl:File .
sld:type sld:null ;
sld:type [ rdfs:label "custom type, check types directory for input format" ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
cwl:valueFrom "${\n return [self.annotation.check_existing ? '--check_existing' : '',\n '--custom',\n [self.annotation.file.path,\n self.annotation.name,\n self.annotation.data_format,\n self.method,\n self.force_report_coordinates ? 1 : 0,\n self.annotation.vcf_fields ? self.annotation.vcf_fields : ''\n ].filter(String).join(',')\n ].filter(String)\n}\n"
] ;
sld:items ;
sld:type sld:array
] .
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ;
sld:type xsd:string .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "Custom allele frequency filter" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ cwl:valueFrom "$(inputs.vcf.path)" ]
[ cwl:valueFrom "$(runtime.outdir)/annotated.af_filtered.vcf" ]
"/usr/bin/perl" "/opt/vep/src/ensembl-vep/filter_vep" "--format" "vcf" "-o"
[ cwl:valueFrom "$(runtime.outdir)/annotated.af_filtered.vcf" ]
) ;
cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/vcf_check.pl" ) ;
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:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/vep_helper-cwl:vep_101.0_v1"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_vcf_basename).vcf.gz" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-i"
] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "SelectVariants (GATK 4.1.8.1)" ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( "-O"
[ cwl:valueFrom "$(runtime.outdir)/variants.tsv" ]
) ;
cwl:arguments ( "-O"
[ cwl:valueFrom "$(runtime.outdir)/variants.tsv" ]
) ;
cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "VariantsToTable" ) ;
cwl:baseCommand ( "/gatk/gatk" "--java-options" "-Xmx4g" "VariantsToTable" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 6000 ;
ResourceRequirement:tmpdirMin 25000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "broadinstitute/gatk:4.1.8.1"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 6000 ;
ResourceRequirement:tmpdirMin 25000
] .
cwl:default "AD" , "AF" , "DP" , "GT" ;
cwl:inputBinding [ CommandLineBinding:position
4 ] ;
cwl:inputBinding [ CommandLineBinding:position
4 ] ;
sld:type [ cwl:inputBinding [ CommandLineBinding:prefix
"-GF" ] ;
sld:items xsd:string ;
sld:type sld:array
] ;
sld:type [ cwl:inputBinding [ CommandLineBinding:prefix
"-GF" ] ;
sld:items xsd:string ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
rdfs:label "Coding Variant filter" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ cwl:valueFrom "$(inputs.vcf.path)" ]
[ cwl:valueFrom "$(runtime.outdir)/annotated.coding_variant_filtered.vcf" ]
"/usr/bin/perl" "/opt/vep/src/ensembl-vep/filter_vep" "--format" "vcf" "-o"
[ cwl:valueFrom "$(runtime.outdir)/annotated.coding_variant_filtered.vcf" ]
"--ontology" "--filter" "Consequence is coding_sequence_variant"
) ;
cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/vcf_check.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/vep_helper-cwl:vep_101.0_v1"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] .
cwl:source .
cwl:source .
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "-ERC"
] ;
sld:type [ sld:symbols , , ;
sld:type sld:enum
] .
cwl:source .
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:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] .
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 ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs ;
cwl:outputs ;
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:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] ;
cwl:stdout "$(inputs.file.basename).gz" .
cwl:default "variants" ;
sld:type xsd:string , sld:null .
cwl:default "Wildtype" , "Downstream" ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.merged_vcf_basename).vcf.gz" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
rdfs:comment "genome assembly to use in vep. Examples: 'GRCh38' or 'GRCm38'" ;
cwl:inputBinding [ CommandLineBinding:position 10 ;
CommandLineBinding:prefix "--assembly"
] ;
sld:type xsd:string .
rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ;
sld:type xsd:string .
sld:type xsd:int , 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 ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , , , , , , , , , , , , , , , ;
cwl:outputs , , , , , ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:SchemaDefRequirement ;
SchemaDefRequirement:types
] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] .
rdfs:comment "an optional string to prepend to the output filename" ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.vcf.basename)" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.vcf.basename)" ] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , xsd:string .
cwl:default true ;
cwl:inputBinding [ CommandLineBinding:position 9 ;
CommandLineBinding:prefix "--everything"
] ;
sld:type xsd:boolean , sld:null .
cwl:in , , , , , , , , , ;
cwl:out , ;
cwl:run .
rdfs:comment "select only a certain type of variants" ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "-select-type"
] ;
sld:type sld:null ;
sld:type [ sld:symbols , ,