@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:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--variant"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.sample)_bam_readcount_snv.tsv" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
-7 ] ;
sld:type cwl:File .
sld:type xsd:int , sld:null .
cwl:source .
cwl:outputSource ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "run vt decompose" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-s" "-o"
[ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ]
) ;
cwl:baseCommand ( "vt" "decompose" ) ;
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 "quay.io/biocontainers/vt:0.57721--hf74b74d_1"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:outputSource ;
sld:type cwl:File .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"decomposed.vcf.gz" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
-5 ] ;
sld:type xsd:string .
cwl:source .
sld:type xsd:int , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.sample)_bam_readcount_indel.tsv" ] ;
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
-4 ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-R"
] ;
sld:type xsd:string .
cwl:source .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
-6 ] ;
sld:type xsd:string .
cwl:source .
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"normalized.vcf.gz" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "run bam-readcount" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position -3 ;
cwl:valueFrom "$(runtime.outdir)"
]
) ;
cwl:baseCommand ( "/usr/bin/python" "/usr/bin/bam_readcount_helper.py" ) ;
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/bam_readcount_helper-cwl:1.0.0"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] ;
cwl:stdout "$(inputs.sample)_bam_readcount.tsv" .
cwl:in , , , , , ;
cwl:out , ;
cwl:run .
cwl:default 20 ;
cwl:inputBinding [ CommandLineBinding:position
-2 ] ;
sld:type xsd:int , sld:null .
cwl:default 0 ;
cwl:inputBinding [ CommandLineBinding:position
-1 ] ;
sld:type xsd:int , sld:null .
sld:type xsd:string .
cwl:source .
a cwl:Workflow ;
rdfs:label "bam_readcount workflow" ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , , ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] .
a cwl:CommandLineTool ;
rdfs:label "Normalize variants" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-o"
[ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "LeftAlignAndTrimVariants" ) ;
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 9000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0"
] .