@prefix LoadListingRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns2: .
@prefix ns1: .
@prefix ns3: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix Dirent: .
@prefix cwl: .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.outSAMunmapped)" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.outSAMunmapped)" ] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "--gcBias"
] ;
sld:type xsd:boolean , sld:null .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--outFileNamePrefix" ;
CommandLineBinding:shellQuote false
] ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--outFileNamePrefix" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--readFilesCommand" ;
CommandLineBinding:shellQuote false
] ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--readFilesCommand" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:string , sld:null .
cwl:default "A" ;
cwl:inputBinding [ CommandLineBinding:position -2 ;
CommandLineBinding:prefix "-l" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"*" ] ;
sld:type cwl:File , sld:null .
sld:type xsd:string , sld:null ;
ns1:x -304 ;
ns1:y -750 .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"Log.progress.out\";\n}\n" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"Log.progress.out\";\n}\n" ] ;
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"ReadsPerGene.out.tab\";\n}\n" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"ReadsPerGene.out.tab\";\n}\n" ] ;
sld:type cwl:File , sld:null .
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 "v1.2" ;
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: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:baseCommand ( "STAR" "--runMode" "alignReads" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/star:2.7.1a--0"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/star:2.7.1a--0"
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , , , ;
cwl:outputs , , , , , , , , ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ Dirent:writable true ;
cwl:entry "$(inputs.genomeDir)"
]
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ Dirent:writable true ;
cwl:entry "$(inputs.genomeDir)"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
a cwl:CommandLineTool ;
ns2:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "salmon" "quant" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "combinelab/salmon:1.1.0"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
rdfs:comment "Name of the directory to write output files in" ;
rdfs:label "Name of the directory to write output files in" ;
cwl:default "STAR" ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:default "A" .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n if (inputs.outSAMtype == \"BAM Unsorted\")\n return p+\"Aligned.out.bam\";\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"Aligned.sortedByCoord.out.bam\";\n}\n" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"${\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 [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
rdfs:comment "path to file that contain input read2" ;
rdfs:label "path to file that contain input read2" ;
cwl:inputBinding [ CommandLineBinding:position
51 ] ;
cwl:inputBinding [ CommandLineBinding:position
51 ] ;
sld:type cwl:File .
cwl:default "Within" .
cwl:source .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.fq)" ] ;
sld:type cwl:File .
rdfs:comment "1\nint: number of threads to run Salmon\n" ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-p" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:int , sld:null .
cwl:default 400 ;
cwl:source .
cwl:default "virus" .
cwl:default true .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.quantdir)" ] ;
sld:type cwl:Directory .
cwl:inputBinding [ CommandLineBinding:position -2 ;
CommandLineBinding:shellQuote false
] ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
0 ] ;
sld:type cwl:File .
cwl:source .
cwl:default "unmapped_1.fq" .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false
] ;
sld:type cwl:File , sld:null .
cwl:source .
cwl:default "unmapped_2.fq" .
cwl:outputBinding [ CommandOutputBinding:glob
"virusAligned.filtered.sortedByCoord.out.bam" ] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-fq"
] ;
sld:type xsd:string .
cwl:source .
cwl:outputSource ;
sld:type cwl:File ;
ns1:x 5.626328e+02 ;
ns1:y -168 .
sld:type cwl:File ;
ns1:x -5.349113e+02 ;
ns1:y -269 .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--outSAMtype" ;
CommandLineBinding:shellQuote false
] ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--outSAMtype" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:default 1 ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--thread"
] ;
sld:type xsd:int , sld:null .
sld:type cwl:Directory ;
ns1:x -3.139492e+02 ;
ns1:y -9.225797e+02 .
cwl:default "BAM SortedByCoordinate" .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.fastq2.basename.replace(/\\.gz$|\\.bz2$/, '').replace(/\\.fq$|\\.fastq$/, '')).fastp.fastq" ] ;
sld:type cwl:File .
cwl:in , , , ;
cwl:out , ;
cwl:run ;
ns1:x -302 ;
ns1:y -343 .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-2" ;
CommandLineBinding:shellQuote false
] ;
sld:type cwl:File .
sld:type xsd:int , sld:null ;
ns1:x -3.663415e+02 ;
ns1:y 3.030909e+02 .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-i"
] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "--validateMappings"
] ;
sld:type xsd:boolean , sld:null .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-@" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:int , sld:null .
cwl:inputBinding [ CommandLineBinding:position
0 ] ;
sld:type cwl:File , sld:null .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-b" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:boolean , sld:null ;
ns1:altPrefix "-b" .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
ns1:x 1.280237e+03 ;
ns1:y -5.737062e+02 .
cwl:default "salmon_quantdir_human" ;
cwl:source .
rdfs:label "STAR mapping: running mapping jobs." ;
cwl:in , , , , , , ;
cwl:out , , , , , , , , ;
cwl:run ;
ns1:x -29 ;
ns1:y -369 .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--length_required"
] ;
sld:type xsd:int , sld:null .
cwl:source .
cwl:default 40 .
rdfs:label "mk_virus_count" ;
cwl:in , ;
cwl:out ;
cwl:run ;
ns1:x 9.632251e+02 ;
ns1:y 4.798781e+02 .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
ns1:x 2.061626e+02 ;
ns1:y -3.943937e+02 .
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:default "Within" ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--outSAMunmapped" ;
CommandLineBinding:shellQuote false
] ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--outSAMunmapped" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:string , sld:null .
rdfs:label "samtools-view" ;
cwl:in , , , , ;
cwl:out ;
cwl:run ;
ns1:x 1.991023e+02 ;
ns1:y 5.259203e+01 .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"Aligned.toTranscriptome.out.bam\";\n}\n" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"Aligned.toTranscriptome.out.bam\";\n}\n" ] ;
sld:type cwl:File , sld:null .
rdfs:label "STAR mapping: running mapping jobs." ;
cwl:in , , , , , ;
cwl:out , , , , , , , , ;
cwl:run ;
ns1:x 6.819188e+02 ;
ns1:y 1.32939e+02 .
cwl:outputBinding [ CommandOutputBinding:glob "${\n var p = inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"Log.final.out\";\n}\n" ;
cwl:loadContents true
] ;
cwl:outputBinding [ CommandOutputBinding:glob "${\n var p = inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"Log.final.out\";\n}\n" ;
cwl:loadContents true
] ;
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.fq2)" ] ;
sld:type cwl:File , sld:null .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-i"
] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
ns1:x 201 ;
ns1:y -114 .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
ns1:x 9.561228e+02 ;
ns1:y 3.914333e+01 .
a cwl:Workflow ;
rdfs:comment "v0.11" ;
rdfs:label "VIRTUS.PE" ;
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 , , , , , , , , , , , , , , , ;
ns1:license "CC BY-NC 4.0" ;
ns1:toolAuthor "Yoshiaki Yasumizu" .
cwl:source .
rdfs:label "bedtools-bamtofastq-pe" ;
cwl:in , , ;
cwl:out , ;
cwl:run ;
ns1:x 4.06143e+02 ;
ns1:y 2.867351e+01 .
cwl:outputBinding [ CommandOutputBinding:glob
"virus_counts.txt" ] ;
sld:type cwl:File .
cwl:default "BAM SortedByCoordinate" .
sld:type xsd:string ;
ns1:x -3.148848e+02 ;
ns1:y -1090 .
cwl:default true .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "mk_virus_count" ;
ns2:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "| cut -f3 | sort | uniq -c | awk '{if ($1>="
]
[ CommandLineBinding:position 2 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom ") print $0}'"
]
) ;
cwl:baseCommand ( "samtools" "view" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.2-0"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:stdout "virus_counts.txt" .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
ns1:x 9.604493e+02 ;
ns1:y 3.311433e+02 .
sld:type xsd:int , sld:null ;
ns1:x 8.051642e+02 ;
ns1:y 6.665659e+02 .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"SJ.out.tab\";\n}\n" ] ;
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 , sld:null ;
ns1:x 5.493676e+02 ;
ns1:y -3.34551e+02 .
cwl:in