@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:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-f"
] ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"per_chromosome_pindel.out" ] ;
sld:type cwl:File .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:secondaryFiles [] ;
sld:type cwl:File .
sld:type xsd:string .
cwl:in , , , , ;
cwl:out , , , , ;
cwl:run .
cwl:source , , , , .
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run .
cwl:secondaryFiles [] ;
sld:type cwl:File .
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"all_INV" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"all_TD" ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
a cwl:Workflow ;
rdfs:label "Per-chromosome 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:outputBinding [ CommandOutputBinding:glob
"all_D" ] ;
sld:type cwl:File .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"all_SI" ] ;
sld:type cwl:File .
cwl:source .
cwl:default 400 ;
sld:type xsd:int .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-c"
] ;
sld:type xsd:string .
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 ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , ;
cwl:outputs , , , , ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:ramMin 64000 ;
ResourceRequirement:tmpdirMin 100000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/cle:v1.3.1"
] .
cwl:outputBinding [ CommandOutputBinding:glob
"all_LI" ] ;
sld:type cwl:File .
cwl:default 400 ;
sld:type xsd:int .
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:outputSource ;
sld:type cwl:File .
cwl:source .