@prefix LoadListingRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns2: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix cwl: .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "samtools_index_bam" ;
ns2:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "samtools" "index" "-b" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biocontainers/samtools:1.3.1"
] ;
cwl:stdout "$(inputs.bam_file.basename).bai" .
rdfs:label "samtools_view" ;
cwl:in ;
cwl:out ;
cwl:run ;
ns1:x 1.503281e+02 ;
ns1:y 1.069531e+02 .
sld:type xsd:string ;
ns1:x 3.776562e+02 ;
ns1:y 1.069531e+02 .
cwl:inputBinding [ CommandLineBinding:position
0 ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "-PL"
] ;
sld:type xsd:string .
a cwl:CommandLineTool ;
rdfs:label "picard_AddOrReplaceReadGroups" ;
ns2:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-O" ;
cwl:valueFrom "$(inputs.sorted_dedup_bam.nameroot).RG.bam"
]
) ;
cwl:baseCommand ( "gatk" "AddOrReplaceReadGroups" ) ;
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 "broadinstitute/gatk:4.1.2.0"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "-LB"
] ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"*_sorted.bam" ] ;
sld:type cwl:File .
sld:type cwl:File ;
ns1:x 0 ;
ns1:y 2.139062e+02 .
cwl:outputSource ;
sld:type cwl:File ;
ns1:x 8.874338e+02 ;
ns1:y 1.604297e+02 .
cwl:outputBinding [ CommandOutputBinding:glob
"*.bam" ] ;
sld:type cwl:File .
cwl:source .
sld:type xsd:string ;
ns1:x 3.776562e+02 ;
ns1:y 2.139062e+02 .
a cwl:Workflow ;
rdfs:label "samtools_picard" ;
ns2: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 .
a cwl:CommandLineTool ;
rdfs:label "samtools_sort" ;
ns2:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-o" ;
cwl:valueFrom "$(inputs.aligned_bam.nameroot)_sorted.bam"
]
) ;
cwl:baseCommand ( "samtools" "sort" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biocontainers/samtools:1.3.1"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
a cwl:CommandLineTool ;
rdfs:label "samtools_view" ;
ns2:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "" ;
cwl:valueFrom "-Sb"
]
) ;
cwl:baseCommand ( "samtools" "view" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biocontainers/samtools:1.3.1"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stdout "$(inputs.aligned_sam.nameroot).bam" .
rdfs:label "samtools_sort" ;
cwl:in ;
cwl:out ;
cwl:run ;
ns1:x 3.776562e+02 ;
ns1:y 0 .
cwl:inputBinding [ CommandLineBinding:position
0 ] ;
sld:type cwl:File .
cwl:source .
rdfs:label "samtools_index_bam" ;
cwl:in ;
cwl:run ;
ns1:x 8.874338e+02 ;
ns1:y 5.347656e+01 .
rdfs:label "picard_AddOrReplaceReadGroups" ;
cwl:in , , , , ;
cwl:out ;
cwl:run ;
ns1:x 5.711719e+02 ;
ns1:y 7.895312e+01 .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "-I"
] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
0 ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"*RG.bam" ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
sld:type xsd:string ;
ns1:x 0 ;
ns1:y 0 .
sld:type xsd:string ;
ns1:x 0 ;
ns1:y 1.069531e+02 .
cwl:inputBinding [ CommandLineBinding:position 10 ;
CommandLineBinding:prefix "-SM"
] ;
sld:type xsd:string .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 8 ;
CommandLineBinding:prefix "-PU"
] ;
sld:type xsd:string .