@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:default 400 ;
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
sld:type xsd:int .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.vcf.basename).gz" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "/bin/cat" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ubuntu:xenial"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] ;
cwl:stdout "per_chromosome_pindel.out" .
cwl:outputBinding [ CommandOutputBinding:glob
"all_INV" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"-p" ] ;
sld:type cwl:File .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position
5 ] ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position 8 ;
CommandLineBinding:prefix "-j"
] ;
sld:type cwl:File , sld:null .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"per_chromosome_pindel.out" ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:default 3 ;
cwl:inputBinding [ CommandLineBinding:prefix
"-e" ] ;
sld:type xsd:int , sld:null .
cwl:source , , , , .
cwl:inputBinding [ CommandLineBinding:prefix
"-r" ] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.vcf.basename)" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:default "pindel.vcf" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-v" ] ;
sld:type xsd:string , sld:null .
cwl:in , , , , , , ;
cwl:out , , , , ;
cwl:run .
cwl:in ;
cwl:out ;
cwl:run .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "pindel v0.2.5b8" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "/usr/bin/perl" "pindel_helper.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/cle:v1.4.2"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 4 ;
ResourceRequirement:ramMin 16000 ;
ResourceRequirement:tmpdirMin 100000
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "#!/usr/bin/perl\n\nuse strict;\nuse warnings;\n\nuse IO::File;\n\nunless (@ARGV > 5) {\n die \"Usage: $0 normal.bam tumor.bam insert_size normal_sample_name tumor_sample_name \";\n}\n\nmy ($normal_bam, $tumor_bam, $insert_size, $normal_name, $tumor_name, @args) = @ARGV;\n\nmy $fh = IO::File->new(\"> pindel.config\");\n\n$fh->say(join(\"\\t\", $normal_bam, $insert_size, $normal_name));\n$fh->say(join(\"\\t\", $tumor_bam, $insert_size, $tumor_name));\n$fh->close;\n\nexit system(qw(/usr/bin/pindel -i pindel.config -w 30 -T 4 -o all), @args);\n" ;
cwl:entryname "pindel_helper.pl"
]
] .
cwl:outputBinding [ CommandOutputBinding:glob
"all_SI" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_name)" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "pindel v0.2.5b8" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-G" "-d" "20161216" ) ;
cwl:baseCommand ( "/usr/bin/pindel2vcf" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 8000 ;
ResourceRequirement:tmpdirMin 100000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/cle:v1.3.1"
] .
cwl:inputBinding [ CommandLineBinding:prefix
"INPUT=" ] ;
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:position 1 ;
cwl:valueFrom "$(self.basename)"
] ;
sld:type cwl:File .
cwl:source .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
cwl:source .
sld:type xsd:string .
a cwl:CommandLineTool ;
rdfs:label "fix vcf header" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "OUTPUT="
[ cwl:valueFrom "$(runtime.outdir)/$(inputs.vcf.basename).gz" ]
) ;
cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "FixVcfHeader" ) ;
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 16000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "broadinstitute/picard:2.23.6"
] .
a cwl:CommandLineTool ;
rdfs:label "vcf index" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
[ CommandLineBinding:shellQuote false ;
cwl:valueFrom " && "
]
"/usr/local/bin/tabix" "-p" "vcf"
) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"all_TD" ] ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run .
cwl:default 400 ;
sld:type xsd:int .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "remove END INFO tags" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-x" "INFO/END" "-Oz" "-o"
[ cwl:valueFrom "$(runtime.outdir)/pindel.noend.vcf.gz" ]
) ;
cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "annotate" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.12"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 4000
] .
cwl:source .
a cwl:Workflow ;
rdfs:label "Run pindel on provided region" ;
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:requirements [ a cwl:SubworkflowFeatureRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] .
cwl:inputBinding [ CommandLineBinding:position
4 ] ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"pindel.noend.vcf.gz" ] ;
sld:type cwl:File .
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 7 ;
CommandLineBinding:prefix "-c"
] ;
sld:type xsd:string , sld:null .
cwl:default "GRCh38DH" ;
sld:type xsd:string , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"all_LI" ] ;
sld:type cwl:File .
cwl:default "pindel.vcf" ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "-f"
] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , xsd:string .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"all_D" ] ;
sld:type cwl:File .
cwl:in , , , ;
cwl:out ;
cwl:run .
cwl:source .
cwl:default "GRCh38DH" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-R" ] ;
sld:type xsd:string , sld:null .
sld:type xsd:string .