@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:outputBinding [ CommandOutputBinding:glob
"all_TD" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--variant"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "SCATTER_COUNT=" ;
CommandLineBinding:separate false
] ;
sld:type xsd:int .
cwl:outputBinding [ CommandOutputBinding:glob
"*.interval.bed" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
rdfs:label "run vt decompose" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-s" "-o"
[ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ]
) ;
cwl:baseCommand ( "vt" "decompose" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-R"
] ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(self.basename)"
] ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(self.basename)"
] ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(self.basename)"
] ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(self.basename)"
] ;
sld:type cwl:File .
cwl:source .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:in , , , ;
cwl:out ;
cwl:run .
cwl:default true .
cwl:outputBinding [ CommandOutputBinding:glob
"all_D" ] ;
sld:type cwl:File .
sld:type xsd:float , sld:null .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-R"
] ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "Sanitize a VCF" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "/bin/bash" "sanitize.sh" ) ;
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/samtools-cwl:1.0.0"
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "set -eou pipefail\n\n# 1) removes lines containing non ACTGN bases, as they conflict with the VCF spec\n# and cause GATK to choke\n# 2) removes mutect-specific format tags containing underscores, which are likewise\n# illegal in the vcf spec\nbase=`basename $1`\noutbase=`echo $base | perl -pe 's/.vcf(.gz)?$//g'`\necho \"$1 $base $outbase\"\nif [[ \"$1\" =~ \".gz\" ]];then\n #gzipped input\n gunzip -c \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nelse\n #non-gzipped input\n cat \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nfi\n/opt/htslib/bin/bgzip $outbase.sanitized.vcf\ntabix -p vcf $outbase.sanitized.vcf.gz\n" ;
cwl:entryname "sanitize.sh"
]
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:ramMin 4000
] .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.file.basename).gz" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.file.basename).gz" ] ;
sld:type cwl:File .
cwl:default 400 ;
sld:type xsd:int .
cwl:source ;
cwl:valueFrom "$(self)_full" .
cwl:outputBinding [ CommandOutputBinding:glob
"per_chromosome_pindel.out" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:default 50 ;
sld:type xsd:int .
cwl:source .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:in , , , , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "/bin/cat" ) ;
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 "ubuntu:xenial"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] ;
cwl:stdout "per_chromosome_pindel.out" .
cwl:in ;
cwl:out ;
cwl:run .
sld:type cwl:File .
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:default 5e-02 ;
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "--min-var-freq"
] ;
sld:type xsd:float , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"pindel.out.vcf" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n if(inputs.vcf.nameext.equals(\".gz\")){\n return inputs.vcf.nameroot.replace(/.vcf$/, \"\") + \".sanitized.vcf.gz\";\n }\n return inputs.vcf.nameroot + \".sanitized.vcf.gz\";\n}\n" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
sld:type cwl:File .
sld:type xsd:string .
cwl:source .
a cwl:Workflow ;
rdfs:label "Per-region pindel" ;
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:MultipleInputFeatureRequirement ] .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--variant"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "remove END INFO tags" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-x" "INFO/END" "-Oz" "-o"
[ cwl:valueFrom "$(runtime.outdir)/pindel.noend.vcf.gz" ]
) ;
cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "annotate" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/cle:v1.3.1"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] .
cwl:source , , , , .
cwl:inputBinding [ CommandLineBinding:prefix
"-f" ] ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"all_INV" ] ;
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run .
cwl:in ;
cwl:out ;
cwl:run .
cwl:valueFrom "pindel" .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
cwl:source .
sld:type xsd:string .
cwl:source .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"all_region_pindel.head" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "SelectVariants (GATK 3.6)" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-o"
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 6000 ;
ResourceRequirement:tmpdirMin 25000
] .
cwl:outputBinding [ CommandOutputBinding:glob
"decomposed.vcf.gz" ] ;
sld:type cwl:File .
cwl:in , , , , , ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "--vcf-file"
] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "pindel v0.2.5b8" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "/usr/bin/perl" "/usr/bin/pindel_helper.pl" "$(inputs.normal_bam.path)" "$(inputs.tumor_bam.path)" "$(inputs.insert_size)" ) ;
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:coresMin 4 ;
ResourceRequirement:ramMin 16000 ;
ResourceRequirement:tmpdirMin 100000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/cle:v1.4.2"
] .
cwl:in ;
cwl:out ;
cwl:run .
cwl:in ;
cwl:out ;
cwl:run .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
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 ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
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/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:stdout "$(inputs.file.basename).gz" .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.vcf.basename)" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.vcf.basename)" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.vcf.basename)" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.vcf.basename)" ] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
a cwl:Workflow ;
rdfs:label "pindel parallel 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:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] .
cwl:inputBinding [ CommandLineBinding:prefix
"-c" ] ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:default 400 ;
sld:type xsd:int .
sld:type xsd:string .
a cwl:Workflow ;
rdfs:label "fp_filter 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 , , , , ,