@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns2: .
@prefix ns1: .
@prefix SecondaryFileSchema: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix cwl: .
@prefix ResourceRequirement: .
rdfs:comment "Version of PFAM to download from https://ftp.ebi.ac.uk/pub/databases/Pfam/releases/" ;
sld:type xsd:string .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "mkdir $(inputs.output_prefix) && rsem-prepare-reference"
]
[ CommandLineBinding:position 9 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "$(inputs.output_prefix)/$(inputs.output_prefix)"
]
[ CommandLineBinding:position 10 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "&& tar -czf $(inputs.output_prefix).tar.gz $(inputs.output_prefix)"
]
) ;
cwl:baseCommand () ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "images.sbgenomics.com/uros_sipetic/rsem:1.3.1"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin "$(inputs.cpu)" ;
ResourceRequirement:ramMin "$(inputs.ram * 1000)"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:source .
cwl:in , , , , ;
cwl:out , , , ;
cwl:run .
rdfs:comment "GB of RAM to allocate to this task." ;
sld:default 16 ;
sld:type xsd:int , sld:null .
rdfs:comment "GTF file. MUST BE UNZIPPED." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--gtf"
] ;
sld:type cwl:File .
rdfs:comment "Version of CTAT fusion dat.gz to download from https://github.com/FusionAnnotator/CTAT_HumanFusionLib/releases" ;
sld:type xsd:string .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:source .
rdfs:comment "Num processing threads to use" ;
sld:default 2 ;
sld:type xsd:int , sld:null .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:outputSource ;
sld:type cwl:File .
rdfs:comment "Version of DFAM to download from https://dfam.org/releases/" ;
sld:type xsd:string .
cwl:in , , ;
cwl:out ;
cwl:run .
rdfs:comment "genome annotation GTF. can be GZIP." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "-g"
] ;
sld:type cwl:File , sld:null .
cwl:in , ;
cwl:out ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"*rna_seq.fa" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:valueFrom "$(\"hla_v\" + inputs.hla_version + \"_gencode_v\" + inputs.gencode_version)\n" .
cwl:source .
cwl:source .
cwl:valueFrom "$(true)" .
cwl:outputBinding [ CommandOutputBinding:glob
"hla.dat" ] ;
sld:type cwl:File .
rdfs:comment "Todays date in the following format: Mar012021 (MonthDayYear)" ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_prefix)/*transcripts.fa" ] ;
sld:type cwl:File .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "tar xf $(inputs.fusion_tar.path) $(inputs.fusion_tar.basename.replace(/.tar.gz$/,\"\"))/fusion_annot_lib.idx $(inputs.fusion_tar.basename.replace(/.tar.gz$/,\"\"))/blast_pairs.idx && tar czf $(inputs.output_basename).tar.gz $(inputs.fusion_tar.basename.replace(/.tar.gz$/,\"\"))/fusion_annot_lib.idx $(inputs.fusion_tar.basename.replace(/.tar.gz$/,\"\"))/blast_pairs.idx"
]
) ;
cwl:baseCommand () ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin "$(inputs.cpu)" ;
ResourceRequirement:ramMin "$(inputs.ram * 1000)"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "ubuntu:24.04"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_filename)" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
rdfs:comment "CPUs to allocate to this task." ;
sld:default 1 ;
sld:type xsd:int , sld:null .
a cwl:CommandLineTool ;
rdfs:comment "Generate star fusion reference. Recommend to run locally as tool will take at least 12 hours to run" ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "tar -I pigz -xvf"
]
[ CommandLineBinding:position 10 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "&& gunzip -c $(inputs.pfam_db.path) > Pfam-A.hmm && hmmpress Pfam-A.hmm"
]
[ CommandLineBinding:position 20 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "&& /usr/local/STAR-Fusion/ctat-genome-lib-builder/prep_genome_lib.pl --pfam_db Pfam-A.hmm --human_gencode_filter"
]
[ CommandLineBinding:position 30 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "$(inputs.resource_manifest ? \"&& cp \" + inputs.resource_manifest.path + \" \" + inputs.output_dir : \"\") && tar -I pigz -cf $(inputs.output_dir).tar.gz $(inputs.output_dir)"
]
) ;
cwl:baseCommand () ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , , , , , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing "$(inputs.ctat_source)" , "$(inputs.genome_fa)" , "$(inputs.reference_gtf)"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin "$(inputs.cpu)" ;
ResourceRequirement:ramMin "$(inputs.ram * 1000)"
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "pgc-images.sbgenomics.com/danmiller/star:fusion-1.10.2"
] .
rdfs:comment "file prefix" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--prefix"
] ;
sld:default "hla" ;
sld:type xsd:string , sld:null .
rdfs:comment "Name for prep_genome_lib output directory. Will also serve as basename for TAR.GZ file." ;
cwl:inputBinding [ CommandLineBinding:position 22 ;
CommandLineBinding:prefix "--output_dir"
] ;
sld:default "star_fusion" ;
sld:type xsd:string .
rdfs:comment "Transcripts Fasta" ;
cwl:inputBinding [ CommandLineBinding:position
9 ] ;
sld:type cwl:File .
rdfs:comment "Num processing threads to use" ;
sld:default 1 ;
sld:type xsd:int , sld:null .
cwl:source .
rdfs:comment "Version of HLA to download from https://github.com/ANHIG/IMGTHLA/releases" ;
sld:type xsd:string .
rdfs:comment "Fasta file to index. Recommend from GENCODE, PRI assembly. MUST BE UNZIPPED" ;
cwl:inputBinding [ CommandLineBinding:position 12 ;
CommandLineBinding:prefix "--genomeFastaFiles"
] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"AnnotFilterRule.pm" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "mkdir $(inputs.genomeDir)"
]
[ CommandLineBinding:position 10 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "&& STAR --runMode genomeGenerate"
]
[ CommandLineBinding:position 20 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "&& tar -czf $(inputs.genomeDir).tar.gz ./$(inputs.genomeDir)"
]
) ;
cwl:baseCommand () ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin "$(inputs.cpu)" ;
ResourceRequirement:ramMin "$(inputs.ram * 1000)"
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "pgc-images.sbgenomics.com/d3b-bixu/star:2.7.10a"
] .
rdfs:comment "Version of CTAT resource SOURCE file to download from https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/" ;
sld:type xsd:string .
rdfs:comment "Version of CTAT fusion dat.gz to download from https://github.com/FusionAnnotator/CTAT_HumanFusionLib/releases" ;
sld:type xsd:string .
rdfs:comment "decompress" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--decompress"
] ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--decompress"
] ;
sld:type xsd:boolean , sld:null .
cwl:source .
rdfs:comment "Num GB memory to make available" ;
sld:default 4 ;
sld:type xsd:int , sld:null .
cwl:valueFrom "$(true)" .
rdfs:comment "Ideal value is read len minus 1, but default 100 ok for most cases" ;
cwl:inputBinding [ CommandLineBinding:position 12 ;
CommandLineBinding:prefix "--sjdbOverhang"
] ;
sld:default 100 ;
sld:type xsd:int , sld:null .
cwl:source .
rdfs:comment "Input GTF file. Can be GZIP." ;
cwl:inputBinding [ CommandLineBinding:position
8 ] ;
cwl:inputBinding [ CommandLineBinding:position
8 ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:source .
rdfs:comment "gene model definitions. MUST BE UNZIPPED" ;
cwl:inputBinding [ CommandLineBinding:position 22 ;
CommandLineBinding:prefix "--gtf"
] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"*primary_assembly.genome.fa.gz" ] ;
sld:type cwl:File .
cwl:in , , , ;
cwl:out , ;
cwl:run .
cwl:outputSource ;
sld:type cwl:File .
rdfs:comment "target AnnotFilterRule.pm, from https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB" ;
cwl:inputBinding [ CommandLineBinding:position 22 ;
CommandLineBinding:prefix "--annot_filter_rule"
] ;
sld:type cwl:File .
cwl:hints [ a ns2:sevenbridges.comAWSInstanceType ] ;
cwl:in , , , , , ;
cwl:out , , , , , , , , ;
cwl:run .
cwl:source .
rdfs:comment "Num processing threads to use" ;
sld:default 2 ;
sld:type xsd:int , sld:null .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( [ CommandLineBinding:position 1 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "kallisto index"
]
) ;
cwl:baseCommand () ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin "$(inputs.cpu)" ;
ResourceRequirement:ramMin "$(inputs.ram * 1000)"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "images.sbgenomics.com/uros_sipetic/kallisto:0.43.1"
] ;
cwl:requirements [ a cwl:ShellCommandRequirement ] .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
a cwl:Workflow ;
rdfs:comment "# GENCODE Reference Builder\n\n## Introduction\n\nGENCODE is a project that aims to identify and classify all gene features in the human genome.\nThe tools of the Kids First RNAseq workflow makes extensive use of GENCODE-based references.\nThese references provide the necessary information to perform read assignment, quanfitifaciton,\nand annoatation of RNAseq data.\n\nGENCODE frequently updates their annotations. Over the past five years, GENCODE has released a\nnew version 2-3 times a year. While version-to-version changes tend to be minor, over the course\nof multiple years, the differences can become significant.\n\nFor large projects, such as Kids First, it's important to have comparable data generated over large\nspans of time. To achieve this we lock our version of GENCODE and generate stable references that\nwill be used for many years.\n\nThe pipeline boils down the creation of the Kids First GENCODE-based references to a series of\nversion declarations. The pipeline will download the appropriate reference file for each version\nprovided and perform the necessary processes with the necessary flags to build the KF references.\n\n### Runtime and Instance Recommendation\n\nIf time is of the essence, we recommend using direct instances to limit retries of longer tasks.\n\nExpected runtime for tools:\n- Under 1 minute: `GTEX_COLLAPSE_ANNOTATION`, `T1K_BUILD`\n- Under 10 minutes: `DOWNLOAD_GENCODE`, `KALLISO_INDEX`\n- Under 2 hours: `RSEM_GENERATE_GENOME`, `STAR_GENERATE_GENOME`\n- 24+ hours: `STAR_FUSION_GENOME_GENERATE`\n\n`STAR_FUSION_GENOME_GENERATE` is an incredibly long running tool. Unfortunately, it seems like\nthere's little motivation to improve that.\n\n### Software Changes\n\nThis pipeline is intended for changes of only the versions of the reference files. Changes in the\nsoftware used to build the GENCODE-based references is not possible in CWL. Currently, the pipeline\nis using the versions of software used in the KF RNAseq pipeline. See the [dockers](./dockers_rnaseq.md).\nIf updating the Dockers of this pipeline, make sure the command line parameters have not changed.\n\n## Usage\n\n### Inputs\n\n- `gencode_version`: Version of GENCODE to download from https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/\n- `ctat_resource_version`: Version of CTAT resource SOURCE file to download from https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/\n- `ctat_fusion_version`: Version of CTAT fusion dat.gz to download from https://github.com/FusionAnnotator/CTAT_HumanFusionLib/releases/\n- `hla_version`: Version of HLA to download from https://github.com/ANHIG/IMGTHLA/releases/\n- `dfam_version`: Version of DFAM to download from https://dfam.org/releases/\n- `pfam_version`: Version of PFAM to download from https://ftp.ebi.ac.uk/pub/databases/Pfam/releases/\n- `date_today`: Todays date in the following format: Mar012021 (MonthDayYear). Used to name output\n\n### Outputs\n\n- `resource_manifest`: This file contains the URLs of all files downloaded. Mostly for recordkeeping purposes, it also ends up in the `star_fusion_genome` TAR\n- `gencode_genome`: GENCODE `*primary_assembly.fa` associated with the `gencode_version`\n- `gencode_annotation`: GENCODE `*primary_assembly.annotation.gtf.gz` associated with the `gencode_version`\n- `gtex_collapsed_annotation_stranded`: Collapsed (i.e., combining all isoforms of a gene into a single transcript) version of `gencode_annotation` created using https://github.com/broadinstitute/gtex-pipeline/tree/master/gene_model with the `--stranded` parameter set\n- `gtex_collapsed_annotation_unstranded`: Collapsed (i.e., combining all isoforms of a gene into a single transcript) version of `gencode_annotation` created using https://github.com/broadinstitute/gtex-pipeline/tree/master/gene_model\n- `rsem_genome`: TAR of transcript references for RSEM created using the `gencode_genome` and `gencode_annotation`\n- `kallisto_idx`: IDX of the transcriptome FASTA within `rsem_genome` for Kallisto\n- `star_genome`: TAR of binary genome sequence, suffix arrays, text chromosome names/lengths, splice junctions coordinates, and transcripts/genes information made using STAR in `--runMode genomeGenerate` from `gencode_genome` and `gencode_annotation`\n- `star_fusion_genome`: STAR fusion genome TAR made from `gencode_genome`, `gencode_annotation`, `ctat_resource_version` SOURCE TAR + filtering rules, `ctat_fusion_version` TAR, `dfam_version` DB, and `pfam_version` DB\n- `star_fusion_annot`: Pared version of `star_fusion_genome` containing only `fusion_annot_lib.idx` and `blast_pairs.idx`. Only used to reduce I/O for fusion annotation steps.\n- `hla_rna_ref_seqs`: T1k HLA reference sequences made using `gencode_annotation` and `hla_version` release DAT file\n- `hla_rna_gene_coords`: T1k HLA reference coordinates made using `gencode_annotation` and `hla_version` release DAT file\n" ;
rdfs:label "GENCODE Ref Builder" ;
ns1:original_cwlVersion "v1.2" ;
ns2:sevenbridges.comcategories "T1K" , "STARFUSION" , "GTEX" , "GENCODE" , "STAR" , "FUSION" , "RSEM" , "KALLISTO" ;
ns2:sevenbridges.comlicense "Apache License 2.0" ;
ns2:sevenbridges.compublisher "KFDRC" ;
Workflow:steps , , , , , , , , , , ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a ns2:sevenbridges.commaxNumberOfParallelInstances ] ;
cwl:inputs , , , , , , , ;
cwl:outputs , , , , , , , , , , , ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
rdfs:comment "GENCODE primary assembly reference fasta file. MUST BE UNZIPPED" ;
cwl:inputBinding [ CommandLineBinding:position 22 ;
CommandLineBinding:prefix "--genome_fa"
] ;
sld:type cwl:File .
cwl:in , , , , , , , , , , ;
cwl:out ;
cwl:run .
rdfs:comment "Reference fasta. MUST BE UNZIPPED." ;
cwl:inputBinding [ CommandLineBinding:position
8 ] ;
sld:type cwl:File .
rdfs:comment "Name for output" ;
sld:default "rsem1.3.1" ;
sld:type xsd:string , sld:null .
rdfs:comment "GB memory to allocate to this task" ;
sld:default 2 ;
sld:type xsd:int , sld:null .
rdfs:comment "Custom GTF.GZ to use rather than GENCODE primary_assembly.annotation.gtf.gz. Must be GZIPPED" ;
sld:type cwl:File , sld:null .
rdfs:comment "Version of CTAT resource SOURCE file to download from https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/" ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.decompress ? inputs.infile.basename.replace(/.gz$/, \"\") : inputs.infile.basename + \".gz\")\n" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.decompress ? inputs.infile.basename.replace(/.gz$/, \"\") : inputs.infile.basename + \".gz\")\n" ] ;
sld:type cwl:File .
cwl:valueFrom "$(true)" .
cwl:outputBinding [ CommandOutputBinding:glob
"*annotation.gtf.gz" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
rdfs:comment "Only collapse transcripts of each gene, do not remove overlaps." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--collapse_only"
] ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--collapse_only"
] ;
sld:type xsd:boolean , sld:null .
cwl:source .
rdfs:comment "IPD-IMGT/HLA or IPD-KIR or user-specified dat file download link" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--download"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "Num GB memory to make available" ;
sld:default 2 ;
sld:type xsd:int , sld:null .
rdfs:comment "Can be extracted from ctat source, for from https://github.com/FusionAnnotator/CTAT_HumanFusionLib/releases" ;
cwl:inputBinding [ CommandLineBinding:position 22 ;
CommandLineBinding:prefix "--fusion_annot_lib"
] ;
sld:type cwl:File .
rdfs:comment "DNA transposable element database (Dfam.hmm), required for repeat masking. Obtain from http://dfam.org/releases/Dfam_3.1/infrastructure/dfamscan/" ;
cwl:inputBinding [ CommandLineBinding:position 22 ;
CommandLineBinding:prefix "--dfam_db"
] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern ".h3i" ;
SecondaryFileSchema:required true
] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern ".h3f" ;
SecondaryFileSchema:required true
] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern ".h3p" ;
SecondaryFileSchema:required true
] ;
cwl:secondaryFiles [ SecondaryFileSchema:pattern ".h3m" ;
SecondaryFileSchema:required true
] ;
sld:type cwl:File .
rdfs:comment "Only consider genes on the same strand when removing overlaps." ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--stranded"
] ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--stranded"
] ;
sld:type xsd:boolean , sld:null .
cwl:in , ;
cwl:out ;
cwl:run .
a cwl:CommandLineTool ;
ns1:original_cwlVersion "v1.2" ;
cwl:arguments ( [ CommandLineBinding:position 0 ;
CommandLineBinding:shellQuote false ;
cwl:valueFrom "/bin/bash download_gencode.sh $(inputs.gencode_version) $(inputs.ctat_resource_version) $(inputs.ctat_fusion_version) $(inputs.hla_version) $(inputs.dfam_version) $(inputs.pfam_version)"
]
) ;
cwl:baseCommand () ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , ,