cwlVersion: v1.0 class: Workflow requirements: - class: StepInputExpressionRequirement - class: InlineJavascriptRequirement inputs: genome_fasta_file: type: File doc: | Genome file in FASTA format, uncompressed annotation_gtf_file: type: File doc: | GTF annotation file make_unique: type: boolean? doc: | Replace repeated target names with unique names kmer_size: type: int? doc: | k-mer (odd) length (default: 31, max value: 31) index_output_filename: type: string? doc: | Filename for the kallisto index to be constructed outputs: transcriptome_fasta_file: type: File outputSource: generate_transcriptome/transcriptome_fasta_file kallisto_index: type: File outputSource: generate_kallisto_index/kallisto_index kallisto_stdout_log: type: File outputSource: generate_kallisto_index/stdout_log kallisto_stderr_log: type: File outputSource: generate_kallisto_index/stderr_log steps: generate_transcriptome: run: ../tools/gffread.cwl in: genome_fasta_file: genome_fasta_file annotation_gtf_file: annotation_gtf_file out: [transcriptome_fasta_file] generate_kallisto_index: run: ../tools/kallisto-index.cwl in: transcriptome_fasta_file: generate_transcriptome/transcriptome_fasta_file make_unique: make_unique kmer_size: kmer_size output_filename: index_output_filename out: - kallisto_index - stdout_log - stderr_log $namespaces: s: http://schema.org/ $schemas: - https://github.com/schemaorg/schemaorg/raw/main/data/releases/11.01/schemaorg-current-http.rdf s:name: "genome-kallisto-index" s:downloadUrl: https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/genome-kallisto-index.cwl s:codeRepository: https://github.com/Barski-lab/workflows s:license: http://www.apache.org/licenses/LICENSE-2.0 s:isPartOf: class: s:CreativeWork s:name: Common Workflow Language s:url: http://commonwl.org/ s:creator: - class: s:Organization s:legalName: "Cincinnati Children's Hospital Medical Center" s:location: - class: s:PostalAddress s:addressCountry: "USA" s:addressLocality: "Cincinnati" s:addressRegion: "OH" s:postalCode: "45229" s:streetAddress: "3333 Burnet Ave" s:telephone: "+1(513)636-4200" s:logo: "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png" s:department: - class: s:Organization s:legalName: "Allergy and Immunology" s:department: - class: s:Organization s:legalName: "Barski Research Lab" s:member: - class: s:Person s:name: Michael Kotliar s:email: mailto:misha.kotliar@gmail.com s:sameAs: - id: http://orcid.org/0000-0002-6486-3898 doc: | Generates a FASTA file with the DNA sequences for all transcripts in a GFF file and builds kallisto index s:about: | Usage: kallisto index [arguments] FASTA-files Required argument: -i, --index=STRING Filename for the kallisto index to be constructed Optional argument: -k, --kmer-size=INT k-mer (odd) length (default: 31, max value: 31) --make-unique Replace repeated target names with unique names