@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:source .
a cwl:Workflow ;
rdfs:label "Detect DoCM variants" ;
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 "vcf index" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
[ CommandLineBinding:shellQuote false ;
cwl:valueFrom " && "
]
"/usr/bin/tabix" "-p" "vcf"
) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] .
cwl:outputSource ;
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run .
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , xsd:string .
cwl:in ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position
4 ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:in , , , ;
cwl:out ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"docm_filter_out.vcf" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , xsd:string .
cwl:inputBinding [ CommandLineBinding:position
5 ] ;
sld:type cwl:File .
cwl:source .
sld:type cwl:File .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"docm_raw_variants.vcf" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(self.basename)"
] ;
sld:type cwl:File .
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 ;
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:stdout "$(inputs.file.basename).gz" .
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.file.basename).gz" ] ;
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run .
a cwl:CommandLineTool ;
rdfs:label "docm filter" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "/usr/bin/perl" "/usr/bin/single_sample_docm_filter.pl" "$(inputs.docm_out.path)" "$(runtime.outdir)" ) ;
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 "mgibio/perl_helper-cwl:1.0.0"
] .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.vcf.basename)" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "HaplotypeCaller (GATK4)" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "/bin/bash" "docm_haplotypeCaller.sh" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\n\n# Running haplotype caller using the newly created interval list\nif [[ \"$#\" == 5 ]];then # If normal_bam is passed.\n # explicitly capturing variables\n reference=$1\n normal_bam=$2\n tumor_bam=$3\n docm_vcf=$4\n interval_list=$5\n # Chaning the interval_list to a new docm_interval_list that spans the docm regions by 200bp\n cat $interval_list | grep '^@' > docm.interval_list # Extracting the header from the interval_list\n zcat $docm_vcf | grep ^chr | awk '{FS = \"\\t\";OFS = \"\\t\";print $1,$2-100,$2+100,\"+\",$1\"_\"$2-100\"_\"$2+100}' >> docm.interval_list # Extracting the docm regions with a 100bp flanking region on both directions\n /gatk/gatk HaplotypeCaller --java-options \"-Xmx8g\" -R $reference -I $normal_bam -I $tumor_bam --alleles $docm_vcf -L docm.interval_list --genotyping-mode GENOTYPE_GIVEN_ALLELES -O docm_raw_variants.vcf\nelse # If normal_bam is not passed\n reference=$1\n tumor_bam=$2\n docm_vcf=$3\n interval_list=$4\n # Chaning the interval_list to a new docm_interval_list that spans the docm regions by 200bp\n cat $interval_list | grep '^@' > docm.interval_list # Extracting the header from the interval_list\n zcat $docm_vcf | grep ^chr | awk '{FS = \"\\t\";OFS = \"\\t\";print $1,$2-100,$2+100,\"+\",$1\"_\"$2-100\"_\"$2+100}' >> docm.interval_list # Extracting the docm regions with a 100bp flanking region on both directions\n /gatk/gatk HaplotypeCaller --java-options \"-Xmx8g\" -R $reference -I $tumor_bam --alleles $docm_vcf -L docm.interval_list --genotyping-mode GENOTYPE_GIVEN_ALLELES -O docm_raw_variants.vcf\nfi\n" ;
cwl:entryname "docm_haplotypeCaller.sh"
]
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 9000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "broadinstitute/gatk:4.1.2.0"
] .