@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns2: .
@prefix ns1: .
@prefix ns3: .
@prefix rdf: .
@prefix Dirent: .
@prefix cwl: .
@prefix CommandLineTool: .
cwl:inputBinding [ CommandLineBinding:position
4 ] ;
sld:type xsd:string .
rdfs:label "STAR mapping: running mapping jobs." ;
cwl:in , , , , , ;
cwl:out , , , , , , , , ;
cwl:run ;
ns1:x 7.539962e+02 ;
ns1:y 1.330281e+02 .
rdfs:label "STAR mapping: running mapping jobs." ;
cwl:in , , , , , , ;
cwl:out , , , , , , , , ;
cwl:run ;
ns1:x -29 ;
ns1:y -369 .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type cwl:File .
cwl:source .
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:default "virus" .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.fq)" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
ns1:x 5.582531e+02 ;
ns1:y -3.370844e+02 .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.prefix).unmapped.bam" ] ;
sld:type cwl:File .
cwl:in , , , ;
cwl:out , ;
cwl:run ;
ns1:x -2.713705e+02 ;
ns1:y -3.58882e+02 .
cwl:source .
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: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 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:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "--gcBias"
] ;
sld:type xsd:boolean , sld:null .
sld:type cwl:Directory ;
ns1:x -305 ;
ns1:y -602 .
a cwl:CommandLineTool ;
rdfs:label "samtools-view" ;
ns2:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "samtools_view_removemulti.sh" ) ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:inputs , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "yyasumizu/bam_filter_polyx:1.1"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:stdout "$(inputs.prefix).unmapped.bam" .
cwl:inputBinding [ CommandLineBinding:position -2 ;
CommandLineBinding:shellQuote false
] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-i"
] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
ns2:original_cwlVersion "v1.0" ;
cwl:arguments ( "-o" "$(inputs.fastq1.basename.replace(/\\.gz$|\\.bz2$/, '').replace(/\\.fq$|\\.fastq$/, '')).fastp.fastq" "-O" "$(inputs.fastq2.basename.replace(/\\.gz$|\\.bz2$/, '').replace(/\\.fq$|\\.fastq$/, '')).fastp.fastq"
[ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "" ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "--trim_poly_x "
]
) ;
cwl:baseCommand ( "fastp" ) ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:inputs , , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/fastp:0.20.0--hdbcaa40_0"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
rdfs:label "mk_summary_virus_count" ;
cwl:in , , ;
cwl:out ;
cwl:run ;
ns1:x 1.132929e+03 ;
ns1:y -5.762986e+02 .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"ReadsPerGene.out.tab\";\n}\n" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"ReadsPerGene.out.tab\";\n}\n" ] ;
sld:type cwl:File , sld:null .
cwl:default 1e-01 ;
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "fastq_pair" ;
ns2:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "fastq_pair" ) ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:inputs , ;
cwl:outputs , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ Dirent:writable true ;
cwl:entry "$(inputs.fq1)"
] ;
cwl:listing [ Dirent:writable true ;
cwl:entry "$(inputs.fq2)"
]
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/fastq-pair:1.0--he1b5a44_1"
] .
cwl:default "unmapped_1.fq" .
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--threshold" ;
CommandLineBinding:shellQuote false
] ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--threshold" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:float , sld:null ;
ns1:toolDefaultValue "0.1" .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "-o" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:string .
cwl:source .
rdfs:label "kz-filter_fq1" ;
cwl:in , , ;
cwl:out ;
cwl:run ;
ns1:x 4.627409e+02 ;
ns1:y 147 .
cwl:inputBinding [ CommandLineBinding:position
0 ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "mk_summary_virus_count" ;
ns2:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "python" "/workdir/mk_summary_virus_count.py" ) ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "yyasumizu/mk_summary_virus_count:1.1"
] .
cwl:default 40 .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.fq2)" ] ;
sld:type cwl:File , sld:null .
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 .
cwl:outputBinding [ CommandOutputBinding:glob
"virus_counts.txt" ] ;
sld:type cwl:File .
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 .
rdfs:label "bam_filter_polyX" ;
cwl:in ;
cwl:out ;
cwl:run ;
ns1:x 8.251763e+02 ;
ns1:y 5.134647e+02 .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
ns1:x 1.280237e+03 ;
ns1:y -5.737062e+02 .
cwl:outputSource ;
sld:type cwl:Directory ;
ns1:x 3.005687e+02 ;
ns1:y -7.156619e+02 .
cwl:default "kz_2.fq" .
cwl:in , , , , , , , ;
cwl:out ;
cwl:run ;
ns1:x 8.566854e+01 ;
ns1:y -7.171351e+02 .
cwl:source .
sld:type xsd:int , sld:null ;
ns1:x -3.864197e+02 ;
ns1:y 2.428753e+02 .
cwl:source .
cwl:default true .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.quantdir)" ] ;
sld:type cwl:Directory .
cwl:source .
cwl:default "salmon_quantdir_human" ;
cwl:source .
cwl:default 400 ;
cwl:source .
sld:type cwl:Directory ;
ns1:x 4.174297e+02 ;
ns1:y 4.527936e+02 .
cwl:outputBinding [ CommandOutputBinding:glob "${\n var p = inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"Log.final.out\";\n}\n" ;
cwl:loadContents true
] ;
cwl:outputBinding [ CommandOutputBinding:glob "${\n var p = inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"Log.final.out\";\n}\n" ;
cwl:loadContents true
] ;
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"*" ] ;
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"${\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 .
sld:type cwl:File ;
ns1:x -4.455146e+02 ;
ns1:y -2.746721e+02 .
cwl:default "Within" .
rdfs:label "kz-filter_fq2" ;
cwl:in , , ;
cwl:out ;
cwl:run ;
ns1:x 4.607409e+02 ;
ns1:y 2.703285e+01 .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
ns1:x 9.548983e+02 ;
ns1:y -1.106729e+02 .
cwl:inputBinding [ CommandLineBinding:position
0 ] ;
sld:type cwl:File .
cwl:default "human" .
cwl:outputSource ;
sld:type cwl:File , sld:null ;
ns1:x 206 ;
ns1:y -5.210446e+02 .
a cwl:CommandLineTool ;
ns2:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "salmon" "quant" ) ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
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:source .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-1" ;
CommandLineBinding:shellQuote false
] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:label "bam_filter_polyX" ;
ns2:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "bam_filter_polyx.sh" ) ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "yyasumizu/bam_filter_polyx:1.2"
] ;
cwl:stdout "virusAligned.filtered.sortedByCoord.out.bam" .
cwl:default 4 ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:int , sld:null .
cwl:default "BAM SortedByCoordinate" .
sld:type xsd:int , sld:null ;
ns1:x 8.051642e+02 ;
ns1:y 6.665659e+02 .
a cwl:CommandLineTool ;
rdfs:label "bedtools-bamtofastq-pe" ;
ns2:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "bedtools" "bamtofastq" ) ;
cwl:cwlVersion ;
cwl:hints [ a ] ;
cwl:hints [ a ] ;
cwl:inputs , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
] .
cwl:inputBinding [ CommandLineBinding:position 6 ;
CommandLineBinding:prefix "--validateMappings"
] ;
sld:type xsd:boolean , sld:null .
rdfs:label "fastq_pair" ;
cwl:in , ;
cwl:out , ;
cwl:run ;
ns1:x 5.77236e+02 ;
ns1:y 9.392457e+01 .
rdfs:comment "path to file that contain input read1" ;
rdfs:label "path to file that contain input read1" ;
cwl:inputBinding [ CommandLineBinding:position 50 ;
CommandLineBinding:prefix "--readFilesIn"
] ;
cwl:inputBinding [ CommandLineBinding:position 50 ;
CommandLineBinding:prefix "--readFilesIn"
] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"Log.progress.out\";\n}\n" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"${\n var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:\"\";\n return p+\"Log.progress.out\";\n}\n" ] ;
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.outSAMunmapped)" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.outSAMunmapped)" ] ;
sld:type cwl:File , sld:null .
cwl:source .
rdfs:comment "Name of the directory to write output files in" ;
rdfs:label "Name of the directory to write output files in" ;
cwl:default "STAR" ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.fq1.basename).paired.fq" ] ;
sld:type cwl:File .
cwl:source .
cwl:default "unmapped_2.fq" .
cwl:outputSource ;
sld:type cwl:File ;
ns1:x 8.621668e+02 ;
ns1:y 3.486447e+02 .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "--length_required"
] ;
sld:type xsd:int , sld:null .
cwl:source .
cwl:default "BAM SortedByCoordinate" .
rdfs:label "prefix" ;
cwl:default "human" ;
sld:type xsd:string , sld:null .
sld:type cwl:File ;
ns1:x -4.469179e+02 ;
ns1:y -4.262689e+02 .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_fq)" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_fq)" ] ;
sld:type cwl:File , sld:null .
cwl:default "A" ;
cwl:inputBinding [ CommandLineBinding:position -2 ;
CommandLineBinding:prefix "-l" ;
CommandLineBinding:shellQuote false
] ;
sld:type xsd:string .