@prefix LoadListingRequirement: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix cwl: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"aligned.sorted.bam" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"reads.2.fastq" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "sort" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "$(inputs.bam_file)"
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/samtools:1.9"
] ;
cwl:stdout "aligned.sorted.bam" .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"*.fa" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"reads.1.fastq" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"*.bam" ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "index" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "$(inputs.bam_file)"
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/samtools:1.9"
] .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
cwl:valueFrom "-b"
]
) ;
cwl:baseCommand ( "view" ) ;
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/samtools:1.9"
] ;
cwl:stdout "aligned.bam" .
cwl:in ;
cwl:out , ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"reference.fa" ] ;
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "I="
] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "bwa" "index" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "$(inputs.reference_file)"
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "biocontainers/bwa:0.7.15"
] .
cwl:source .
cwl:outputSource ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:source .
a cwl:Workflow ;
rdfs:label "alignment workflow" ;
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:source .
cwl:source .
cwl:outputSource ;
sld:type cwl:File .
rdfs:comment "gzipped reference fasta to align to" ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"aligned.bam" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
sld:type cwl:File .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "FASTQ=" ;
cwl:valueFrom "reads.1.fastq"
]
[ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "SECOND_END_FASTQ=" ;
cwl:valueFrom "reads.2.fastq"
]
) ;
cwl:baseCommand ( "SamToFastq" ) ;
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/picard:2.18.2"
] .
cwl:source .
rdfs:comment "bam file to align" ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"*.fa" ] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "-c" ) ;
cwl:baseCommand ( "gunzip" ) ;
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:stdout "reference.fa" .
cwl:outputBinding [ CommandOutputBinding:glob
"aligned.sam" ] ;
sld:type cwl:File .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
cwl:in ;
cwl:out ;
cwl:run .
cwl:in ;
cwl:out ;
cwl:run .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "faidx" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "$(inputs.reference_file)"
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/samtools:1.9"
] .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "bwa" "mem" ) ;
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/bwa:0.7.15"
] ;
cwl:stdout "aligned.sam" .