@prefix LoadListingRequirement: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix cwl: .
@prefix sld: .
@prefix ResourceRequirement: .
@prefix CommandOutputBinding: .
@prefix ns1: .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "flagstat $(inputs.input_bam.path) -@ 4 > $(inputs.input_bam.nameroot).flagstat"
]
) ;
cwl:baseCommand ( "samtools" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 4 ;
ResourceRequirement:ramMin 4000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "pgc-images.sbgenomics.com/d3b-bixu/samtools:1.20-multi-arch"
] .
cwl:in ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) .
sld:type cwl:File .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"*.flagstat" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
a cwl:Workflow ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] .