@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns2: .
@prefix ns1: .
@prefix ns3: .
@prefix SecondaryFileSchema: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix Dirent: .
@prefix cwl: .
sld:default true .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-r" ;
CommandLineBinding:shellQuote false
] ;
sld:type cwl:File .
sld:type cwl:Directory ;
ns1:x -619 ;
ns1:y -446 .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "--validateMappings"
] ;
sld:type xsd:boolean , sld:null .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
ns1:x -7.795968e+01 ;
ns1:y -1.07879e+02 .
cwl:inputBinding [ CommandLineBinding:position -2 ;
CommandLineBinding:prefix "-i" ;
CommandLineBinding:shellQuote false
] ;
sld:type cwl:Directory .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"SJ.out.tab\";\n}\n" ] ;
sld:type cwl:File , sld:null .
cwl:outputSource ;
sld:type cwl:File ;
ns1:x -6.572579e+01 ;
ns1:y 26 .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"Aligned.toTranscriptome.out.bam\";\n}\n" ] ;
sld:type cwl:File , sld:null .
a cwl:CommandLineTool ;
ns2:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "salmon" "quant" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:LoadListingRequirement ;
cwl:loadListing "deep_listing"
] ;
cwl:hints [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "combinelab/salmon:1.1.0"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--outSAMtype" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:string , sld:null .
rdfs:comment "1\nint: number of threads to run Salmon\n" ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-p" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:int , sld:null .
sld:default "A" .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"Log.progress.out\";\n}\n" ] ;
sld:type cwl:File , sld:null .
rdfs:comment "1st word: None: no output, Within: output unmapped reads within the main SAM file (i.e. Aligned.out.sam). 2nd word: KeepPairs: record unmapped mate for each alignment, and, in case of unsorted output, keep it adjacent to its mapped mate. Only a↵ects multi-mapping reads." ;
rdfs:label "output of unmapped reads in the SAM format" ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--outSAMunmapped" ;
CommandLineBinding:shellQuote false
] ;
sld:default "Within" ;
sld:type xsd:string , sld:null .
rdfs:comment "path to file that contain input read" ;
rdfs:label "path to file that contain input read" ;
cwl:inputBinding [ CommandLineBinding:position 50 ;
CommandLineBinding:prefix "--readFilesIn"
] ;
sld:type cwl:File .
sld:type cwl:Directory ;
ns1:x -631 ;
ns1:y -699 .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
ns1:x -7.585483e+01 ;
ns1:y -2.362504e+02 .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--readFilesCommand" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "--gcBias"
] ;
sld:type xsd:boolean , sld:null .
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "-o" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:string .
sld:default true .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n if (inputs.outSAMtype == \"BAM Unsorted\")\n return p+\"Aligned.out.bam\";\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"Aligned.sortedByCoord.out.bam\";\n}\n" ] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern
"${\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return [\n {\"path\": p+\"Log.final.out\", \"class\":\"File\"},\n {\"path\": p+\"SJ.out.tab\", \"class\":\"File\"},\n {\"path\": p+\"Log.out\", \"class\":\"File\"}\n ];\n}\n" ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
a cwl:Workflow ;
rdfs:comment "STAR mapping and salmon quantification for one specified virus. Prepare using create_singlevirus.cwl beforehand. VIRTUS version 1.0" ;
rdfs:label "VIRTUS.SE.singlevirus" ;
ns2:original_cwlVersion "v1.1" ;
Workflow:steps , ;
cwl:cwlVersion ;
cwl:inputs , , , , , ;
cwl:outputs , , , , ;
ns1:toolAuthor "Yoshiaki Yasumizu" .
rdfs:comment "defines the number of threads to be used for genome generation, it has to be set to the number of available cores on the server node." ;
rdfs:label "Number of threads" ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--runThreadN" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:int , sld:null .
cwl:source .
cwl:in , , , , , , ;
cwl:out ;
cwl:run ;
ns1:x -3.523952e+02 ;
ns1:y -5.721289e+02 .
rdfs:comment "Name of the directory to write output files in" ;
rdfs:label "Name of the directory to write output files in" ;
sld:default "STAR" ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position -2 ;
CommandLineBinding:prefix "-l" ;
CommandLineBinding:shellQuote false
] ;
sld:default "A" ;
sld:type xsd:string .
rdfs:label "STAR mapping: running mapping jobs." ;
cwl:in , , , , ;
cwl:out , , , , , , , , ;
cwl:run ;
ns1:x -3.107177e+02 ;
ns1:y -2.230083e+02 .
sld:type xsd:string , sld:null ;
ns1:x -622 ;
ns1:y -568 .
cwl:outputBinding [ CommandOutputBinding:glob
"${ var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\"; return p+\"Log.out\"; }" ] ;
sld:type cwl:File , sld:null .
sld:type xsd:string ;
ns1:x -631 ;
ns1:y -821 .
rdfs:comment "path to the directory where genome files are stored" ;
rdfs:label "path to the directory where genome files are stored" ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--genomeDir" ;
CommandLineBinding:shellQuote false
] ;
sld:type cwl:Directory .
cwl:outputBinding [ CommandOutputBinding:glob "${\n var p = inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"Log.final.out\";\n}\n" ;
cwl:loadContents true
] ;
sld:type cwl:File , sld:null .
a cwl:CommandLineTool ;
rdfs:comment "STAR: Spliced Transcripts Alignment to a Reference. https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf" ;
rdfs:label "STAR mapping: running mapping jobs." ;
ns2:original_cwlVersion "v1.0" ;
ns3:author [ a ns3:Person ;
ns3:email "mailto:inutano@gmail.com" ;
ns3:identifier "https://orcid.org/0000-0003-3777-5945" ;
ns3:name "Tazro Ohta"
] ;
ns3:codeRepository "https://github.com/pitagora-network/pitagora-cwl" ;
ns3:license "https://spdx.org/licenses/Apache-2.0" ;
cwl:baseCommand ( "STAR" "--runMode" "alignReads" ) ;
cwl:cwlVersion ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/star:2.7.1a--0"
] ;
cwl:hints [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:LoadListingRequirement ;
cwl:loadListing "deep_listing"
] ;
cwl:inputs , , , , , , , ;
cwl:outputs , , , , , , , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ Dirent:writable true ;
cwl:entry "$(inputs.genomeDir)"
]
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
ns1:x -7.889516e+01 ;
ns1:y -3.880565e+02 .
sld:type cwl:File ;
ns1:x -6.322097e+02 ;
ns1:y 1.279193e+02 .
sld:type xsd:int , sld:null ;
ns1:x -632 ;
ns1:y -24 .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n if (inputs.bamRemoveDuplicatesType != \"UniqueIdentical\")\n return null;\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"Processed.out.bam\";\n}\n" ] ;
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"ReadsPerGene.out.tab\";\n}\n" ] ;
sld:type cwl:File , sld:null .
sld:default "BAM SortedByCoordinate " .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.outSAMunmapped)" ] ;
sld:type cwl:File , sld:null .
cwl:outputSource ;
sld:type cwl:Directory ;
ns1:x -1.13242e+02 ;
ns1:y -6.082741e+02 .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.quantdir)" ] ;
sld:type cwl:Directory .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--outFileNamePrefix" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:string , sld:null .