@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:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "False Positive filter" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output"
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ]
) ;
cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ;
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/fp_filter-cwl:1.0.1"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 6000 ;
ResourceRequirement:tmpdirMin 25000
] .
sld:type xsd:float , sld:null .
rdfs:comment "select only a certain type of variants" ;
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "-selectType"
] ;
sld:type sld:null ;
sld:type [ sld:symbols , , , , , ;
sld:type sld:enum
] .
cwl:source .
cwl:source ;
cwl:valueFrom "$(self)_filtered" .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--variant"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "--vcf-file"
] ;
sld:type cwl:File .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:in , , , , ;
cwl:out , ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "--excludeFiltered"
] ;
sld:type xsd:boolean , sld:null .
sld:type xsd:string .
sld:type cwl:File .
cwl:source .
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
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\n/usr/bin/tabix -p vcf $outbase.sanitized.vcf.gz\n" ;
cwl:entryname "sanitize.sh"
]
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:ramMin 4000
] .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n if(inputs.vcf.nameext.equals(\".gz\")){\n return inputs.vcf.nameroot.replace(/.vcf$/, \"\") + \".sanitized.vcf.gz\";\n }\n return inputs.vcf.nameroot + \".sanitized.vcf.gz\";\n}\n" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source ;
cwl:valueFrom "$(self)_full" .
cwl:default true .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.merged_vcf_basename).vcf.gz" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"normalized.vcf.gz" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:default true .
cwl:in ;
cwl:out ;
cwl:run .
cwl:source .
cwl:valueFrom "mutect" .
a cwl:CommandLineTool ;
rdfs:label "Mutect2 (GATK 4)" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
cwl:valueFrom "mutect.vcf.gz"
]
) ;
cwl:baseCommand ( "/bin/bash" "Mutect2.sh" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\n\nexport tumor_bam=\"$3\"\nexport normal_bam=\"$4\"\n\nTUMOR=`perl -e 'my $header_str = qx(samtools view -H $ENV{tumor_bam}); my ($sample_name) = $header_str =~ /SM:([ -~]+)/; print $sample_name'` #Extracting the sample name from the TUMOR bam.\nNORMAL=`perl -e 'my $header_str = qx(samtools view -H $ENV{normal_bam}); my ($sample_name) = $header_str =~ /SM:([ -~]+)/; print $sample_name'` #Extracting the sample name from the NORMAL bam.\n/gatk/gatk Mutect2 --java-options \"-Xmx20g\" -O $1 -R $2 -I $3 -tumor \"$TUMOR\" -I $4 -normal \"$NORMAL\" -L $5 #Running Mutect2.\n/gatk/gatk FilterMutectCalls -R $2 -V mutect.vcf.gz -O mutect.filtered.vcf.gz #Running FilterMutectCalls on the output vcf.\n" ;
cwl:entryname "Mutect2.sh"
]
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 32000 ;
ResourceRequirement:tmpdirMin 100000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "broadinstitute/gatk:4.1.2.0"
] .
cwl:default "merged" ;
sld:type xsd:string , sld:null .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "SelectVariants (GATK 3.6)" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-o"
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 6000 ;
ResourceRequirement:tmpdirMin 25000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0"
] .
cwl:default 5e-02 ;
cwl:inputBinding [ CommandLineBinding:position 5 ;
CommandLineBinding:prefix "--min-var-freq"
] ;
sld:type xsd:float , sld:null .
cwl:in ;
cwl:out ;
cwl:run .
a cwl:CommandLineTool ;
rdfs:label "Normalize variants" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-o"
[ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "LeftAlignAndTrimVariants" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
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"
] .
cwl:in , , , , , ;
cwl:out ;
cwl:run .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--variant"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:source .
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
sld:type xsd:string .
a cwl:CommandLineTool ;
rdfs:label "vcf index" ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
[ CommandLineBinding:shellQuote false ;
cwl:valueFrom " && "
]
"/usr/bin/tabix" "-p" "vcf"
) ;
cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
[ CommandLineBinding:shellQuote false ;
cwl:valueFrom " && "
]
"/usr/bin/tabix" "-p" "vcf"
) ;
cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
[ CommandLineBinding:shellQuote false ;
cwl:valueFrom " && "
]
"/usr/bin/tabix" "-p" "vcf"
) ;
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:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
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:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0"
] .
sld:type cwl:File .
cwl:in , ;
cwl:out ;
cwl:run .
a cwl:Workflow ;
rdfs:label "mutect 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:SubworkflowFeatureRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] .
a cwl:CommandLineTool ;
rdfs:label "bgzip VCF" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-c" ) ;
cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ;
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/samtools-cwl:1.0.0"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] ;
cwl:stdout "$(inputs.file.basename).gz" .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:secondaryFiles [] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
rdfs:label "vcf merge" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "--allow-overlaps" "--remove-duplicates" "--output-type" "z" "-o"
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.merged_vcf_basename).vcf.gz" ]
) ;
cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "concat" ) ;
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/bcftools-cwl:1.3.1"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] .
cwl:source .
cwl:source .
cwl:source .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-L"
] ;
sld:type cwl:File , sld:null .
cwl:source .
sld:type xsd:int .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_vcf_basename).vcf.gz" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "INPUT=" ;
CommandLineBinding:separate false
] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--bam-file"
] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--reference"
] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , xsd:string .
a cwl:CommandLineTool ;
rdfs:label "CombineVariants for Panel of Normals" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-minN" "2" "--setKey" "null" "--filteredAreUncalled" "--filteredrecordsmergetype" "KEEP_IF_ANY_UNFILTERED" "-o"
[ cwl:valueFrom "$(runtime.outdir)/panel_of_normals.vcf.gz" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "CombineVariants" ) ;
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 ;
ResourceRequirement:tmpdirMin 25000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0"
] .
cwl:default "fpfilter" ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:source .
cwl:default "TUMOR" ;
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "--sample"
] ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "-L"
] ;
sld:type cwl:File , sld:null .
a cwl:Workflow ;
rdfs:label "mutect panel-of-normals 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