@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 ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
sld:type xsd:string .
sld:type xsd:string .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"refAlign.bam" ] ;
sld:type cwl:File .
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
a cwl:Workflow ;
rdfs:label "Unaligned to aligned BAM" ;
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:ScatterFeatureRequirement ] .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type xsd:string .
sld:type xsd:string .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "align with bwa_mem and tag" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 4 ;
cwl:valueFrom "$(runtime.cores)"
]
) ;
cwl:baseCommand ( "/bin/bash" "/usr/bin/alignment_helper.sh" ) ;
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/alignment_helper-cwl:1.0.0"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 8 ;
ResourceRequirement:ramMin 20000
] ;
cwl:stdout "refAlign.bam" .