@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:in , , ;
cwl:out ;
cwl:run ;
ns1:x -2.663377e+02 ;
ns1:y -3.326101e+02 .
cwl:outputBinding [ CommandOutputBinding:glob
"*" ] ;
sld:type cwl:File , sld:null .
cwl:default "A" ;
cwl:inputBinding [ CommandLineBinding:position -2 ;
CommandLineBinding:prefix "-l" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:string .
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"
] ;
cwl:inputBinding [ CommandLineBinding:position 50 ;
CommandLineBinding:prefix "--readFilesIn"
] ;
sld:type cwl:File .
sld:type cwl:File ;
ns1:x -4.339359e+02 ;
ns1:y -3.132906e+02 .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
ns1:x 8.892903e+02 ;
ns1:y 2.57067e+01 .
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 .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--length_required"
] ;
sld:type xsd:int , sld:null .
rdfs:label "STAR mapping: running mapping jobs." ;
cwl:in , , , , ;
cwl:out , , , , , , , , ;
cwl:run ;
ns1:x 7.433086e+00 ;
ns1:y -4.240473e+02 .
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:default true .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-fq"
] ;
sld:type xsd:string .
cwl:default "salmon_quantdir_human" ;
cwl:source .
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:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "--validateMappings"
] ;
sld:type xsd:boolean , sld:null .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
ns1:x 2.40662e+02 ;
ns1:y -4.9993e+02 .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position -2 ;
CommandLineBinding:shellQuote false
] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "--gcBias"
] ;
sld:type xsd:boolean , sld:null .
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:source .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
ns1:x 1.280237e+03 ;
ns1:y -5.737062e+02 .
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:inputBinding [ CommandLineBinding:position
0 ] ;
sld:type cwl:File .
cwl:default 4 .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false
] ;
sld:type cwl:File , sld:null .
sld:type cwl:Directory ;
ns1:x -305 ;
ns1:y -602 .
cwl:inputBinding [ CommandLineBinding:position -2 ;
CommandLineBinding:prefix "-i" ;
CommandLineBinding:shellQuote false
] ;
sld:type cwl:Directory .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
ns1:x 8.487875e+02 ;
ns1:y -1.041099e+02 .
cwl:outputBinding [ CommandOutputBinding:glob
"virusAligned.filtered.sortedByCoord.out.bam" ] ;
sld:type cwl:File , sld:null .
cwl:source .
cwl:default 400 ;
cwl:source .
a cwl:CommandLineTool ;
ns3:original_cwlVersion "v1.0" ;
cwl:arguments ( "-o" "$(inputs.fastq.basename.replace(/\\.gz$|\\.bz2$/, '').replace(/\\.fq$|\\.fastq$/, '')).fastp.fastq"
[ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "" ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "--trim_poly_x "
]
) ;
cwl:baseCommand ( "fastp" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/fastp:0.20.0--hdbcaa40_0"
] .
cwl:default "A" .
cwl:outputSource ;
sld:type cwl:File ;
ns1:x 412 ;
ns1:y 218 .
sld:type cwl:Directory ;
ns1:x -3.139492e+02 ;
ns1:y -9.225797e+02 .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type cwl:File .
cwl:default "BAM SortedByCoordinate" .
cwl:source .
cwl:default "unmapped.fq" .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-@" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:int , sld:null .
sld:type cwl:Directory ;
ns1:x 4.472225e+02 ;
ns1:y -2.63028e+02 .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--readFilesCommand" ;
CommandLineBinding:shellQuote false
] ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--readFilesCommand" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:string , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.quantdir)" ] ;
sld:type cwl:Directory .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
0 ] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-b" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:boolean , sld:null ;
ns1:altPrefix "-b" .
cwl:source .
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:source .
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 .
cwl:source .
cwl:source .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
ns1:x 9.497107e+02 ;
ns1:y 2.827711e+02 .
cwl:source .
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
"${\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"SJ.out.tab\";\n}\n" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"SJ.out.tab\";\n}\n" ] ;
sld:type cwl:File , sld:null .
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "-o" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:string .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
ns1:x 2.627429e+02 ;
ns1:y -3.69516e+02 .
cwl:outputSource ;
sld:type cwl:Directory ;
ns1:x 2.419546e+02 ;
ns1:y -6.7218e+02 .
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "bedtools-bamtofastq-pe" ;
ns3:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "bedtools" "bamtofastq" ) ;
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 "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.fq)" ] ;
sld:type cwl:File .
cwl:default "virus" .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n if (inputs.bamRemoveDuplicatesType != \"UniqueIdentical\")\n return null;\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"Processed.out.bam\";\n}\n" ] ;
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:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-r" ;
CommandLineBinding:shellQuote false
] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-i"
] ;
sld:type cwl:File .
a cwl:Workflow ;
rdfs:comment "v0.11" ;
rdfs:label "VIRTUS.SE" ;
ns3: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 , , , , , , , , , , , , ;
ns1:license "CC BY-NC 4.0" ;
ns1:links ;
ns1:toolAuthor "Yoshiaki Yasumizu" .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-i"
] ;
sld:type cwl:File .
sld:type xsd:int , sld:null ;
ns1:x 7.389225e+02 ;
ns1:y 5.196523e+02 .
sld:type xsd:int , sld:null ;
ns1:x -3.663415e+02 ;
ns1:y 3.030909e+02 .
sld:type xsd:string , sld:null ;
ns1:x -3.176976e+02 ;
ns1:y -7.417814e+02 .
cwl:outputBinding [ CommandOutputBinding:glob
"virus_counts.txt" ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
rdfs:label "bam_filter_polyX" ;
cwl:in ;
cwl:out ;
cwl:run ;
ns1:x 8.476025e+02 ;
ns1:y 3.6641e+02 .
a cwl:CommandLineTool ;
rdfs:label "mk_virus_count" ;
ns3: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 $0}'"
]
) ;
cwl:baseCommand ( "samtools" "view" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.2-0"
] ;
cwl:stdout "virus_counts.txt" .
sld:type xsd:string ;
ns1:x -3.148848e+02 ;
ns1:y -1090 .
cwl:default 1 ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--thread"
] ;
sld:type xsd:int , sld:null .
cwl:default "human" .
cwl:default 40 .
cwl:default "BAM SortedByCoordinate" .
rdfs:label "bedtools-bamtofastq-pe" ;
cwl:in , ;
cwl:out ;
cwl:run ;
ns1:x 3.921209e+02 ;
ns1:y -1.100016e+02 .
rdfs:label "" .
rdfs:label "prefix" ;
sld:type xsd:string , sld:null .
cwl:default true .
a cwl:CommandLineTool ;
rdfs:label "samtools-view" ;
ns3:original_cwlVersion "v1.0" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix ""
]
) ;
cwl:baseCommand ( "samtools" "view" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.2-0"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:stdout "$(inputs.prefix).unmapped.bam" .
a cwl:CommandLineTool ;
rdfs:label "bam_filter_polyX" ;
ns3:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "bam_filter_polyx.sh" ) ;
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 "yyasumizu/bam_filter_polyx:latest"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:stdout "virusAligned.filtered.sortedByCoord.out.bam" .
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 .
cwl:in , , , , , , ;
cwl:out ;
cwl:run ;
ns1:x -1.050771e+01 ;
ns1:y -6.712449e+02 .
rdfs:label "samtools-view" ;
cwl:in , , , , ;
cwl:out ;
cwl:run ;
ns1:x 1.991023e+02 ;
ns1:y 5.259203e+01 .
a cwl:CommandLineTool ;
ns3: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:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "combinelab/salmon:1.1.0"
] .
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
] ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--genomeDir" ;
CommandLineBinding:shellQuote false
] ;
sld:type cwl:Directory .
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
] ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--runThreadN" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:int , sld:null .
cwl:outputSource ;
sld:type cwl:File ;
ns1:x 1.973414e+02 ;
ns1:y -1.088477e+02 .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
ns1:x 2.766432e+02 ;
ns1:y -2.308994e+02 .