cwlVersion: v1.0 class: Workflow requirements: - class: SubworkflowFeatureRequirement - class: StepInputExpressionRequirement - class: InlineJavascriptRequirement - class: MultipleInputFeatureRequirement 'sd:metadata': - "../metadata/rnaseq-header.cwl" inputs: star_indices_folder: type: Directory label: "STAR indices folder for reference genome" doc: "Path to STAR generated indices for reference genome" insilico_star_indices_folder: type: Directory label: "STAR indices folder for insilico genome" doc: "Path to STAR generated indices for insilico genome" chrom_length_file: type: File label: "Chromosome length file for reference genome" format: "http://edamontology.org/format_2330" doc: "Chromosome length file for reference genome" strain1: type: string label: "I strain name" doc: "First strain name" strain2: type: string label: "II strain name" doc: "Second strain name" strain1_chain_file: type: File label: "I strain chain file" format: "http://edamontology.org/format_2330" doc: "Chain file to project strain I to reference genome" strain2_chain_file: type: File label: "II strain chain file" format: "http://edamontology.org/format_2330" doc: "Chain file to project strain II to reference genome" threads: type: int? default: 2 label: "Number of threads" doc: "Number of threads for those steps that support multithreading" fastq_file_upstream: type: File label: "FASTQ upstream input file" format: "http://edamontology.org/format_1930" doc: "Upstream reads data in a FASTQ format, received after paired end sequencing" fastq_file_downstream: type: File label: "FASTQ downstream input file" format: "http://edamontology.org/format_1930" doc: "Downstream reads data in a FASTQ format, received after paired end sequencing" outputs: strain1_bigwig: type: File format: "http://edamontology.org/format_3006" label: "I strain bigWig file" doc: "Generated bigWig file for the first strain" outputSource: allele_vcf_alignreads_se_pe/strain1_bigwig strain2_bigwig: type: File format: "http://edamontology.org/format_3006" label: "II strain bigWig file" doc: "Generated bigWig file for the second strain" outputSource: allele_vcf_alignreads_se_pe/strain2_bigwig reference_bigwig: type: File format: "http://edamontology.org/format_3006" label: "Reference bigWig file" doc: "Generated BigWig file for the reference genome" outputSource: allele_vcf_alignreads_se_pe/reference_bigwig strain1_bambai_pair: type: File format: "http://edamontology.org/format_2572" label: "Strain I coordinate sorted BAM alignment file (+index BAI)" doc: "Coordinate sorted BAM file and BAI index file for strain I" outputSource: allele_vcf_alignreads_se_pe/strain1_bambai_pair strain2_bambai_pair: type: File format: "http://edamontology.org/format_2572" label: "Strain II coordinate sorted BAM alignment file (+index BAI)" doc: "Coordinate sorted BAM file and BAI index file for strain II" outputSource: allele_vcf_alignreads_se_pe/strain2_bambai_pair reference_bambai_pair: type: File format: "http://edamontology.org/format_2572" label: "Reference coordinate sorted BAM alignment file (+index BAI)" doc: "Coordinate sorted BAM file and BAI index file for reference genome" outputSource: allele_vcf_alignreads_se_pe/reference_bambai_pair insilico_star_final_log: type: File format: "http://edamontology.org/format_2330" label: "STAR final log for insilico genome" doc: "STAR Log.final.out for insilico genome" outputSource: allele_vcf_alignreads_se_pe/insilico_star_final_log insilico_star_out_log: type: File? format: "http://edamontology.org/format_2330" label: "STAR log out for insilico genome" doc: "STAR Log.out for insilico genome" outputSource: allele_vcf_alignreads_se_pe/insilico_star_out_log insilico_star_progress_log: type: File? format: "http://edamontology.org/format_2330" label: "STAR progress log for insilico genome" doc: "STAR Log.progress.out for insilico genome" outputSource: allele_vcf_alignreads_se_pe/insilico_star_progress_log insilico_star_stdout_log: type: File? format: "http://edamontology.org/format_2330" label: "STAR stdout log for insilico genome" doc: "STAR Log.std.out for insilico genome" outputSource: allele_vcf_alignreads_se_pe/insilico_star_stdout_log reference_star_final_log: type: File format: "http://edamontology.org/format_2330" label: "STAR final log for reference genome" doc: "STAR Log.final.out for reference genome" outputSource: allele_vcf_alignreads_se_pe/reference_star_final_log reference_star_out_log: type: File? format: "http://edamontology.org/format_2330" label: "STAR log out for reference genome" doc: "STAR Log.out for reference genome" outputSource: allele_vcf_alignreads_se_pe/reference_star_out_log reference_star_progress_log: type: File? format: "http://edamontology.org/format_2330" label: "STAR progress log for reference genome" doc: "STAR Log.progress.out for reference genome" outputSource: allele_vcf_alignreads_se_pe/reference_star_progress_log reference_star_stdout_log: type: File? format: "http://edamontology.org/format_2330" label: "STAR stdout log for reference genome" doc: "STAR Log.std.out for reference genome" outputSource: allele_vcf_alignreads_se_pe/reference_star_stdout_log steps: extract_fastq_upstream: run: ../tools/extract-fastq.cwl in: compressed_file: fastq_file_upstream out: [fastq_file] extract_fastq_downstream: run: ../tools/extract-fastq.cwl in: compressed_file: fastq_file_downstream out: [fastq_file] allele_vcf_alignreads_se_pe: run: ../subworkflows/allele-vcf-alignreads-se-pe.cwl in: fastq_files: [extract_fastq_upstream/fastq_file, extract_fastq_downstream/fastq_file] insilico_star_indices_folder: insilico_star_indices_folder reference_star_indices_folder: star_indices_folder reference_chrom_length_file: chrom_length_file strain1: strain1 strain2: strain2 strain1_chain_file: strain1_chain_file strain2_chain_file: strain2_chain_file threads: threads out: - strain1_bambai_pair - strain2_bambai_pair - reference_bambai_pair - strain1_bigwig - strain2_bigwig - reference_bigwig - insilico_star_final_log - insilico_star_out_log - insilico_star_progress_log - insilico_star_stdout_log - reference_star_final_log - reference_star_out_log - reference_star_progress_log - reference_star_stdout_log $namespaces: s: http://schema.org/ $schemas: - http://schema.org/docs/schema_org_rdfa.html s:name: "RNA-seq (VCF) alelle specific pipeline for paired-end data" label: "RNA-seq (VCF) alelle specific pipeline for paired-end data" s:alternateName: "Allele specific RNA-Seq (using vcf) paired-end workflow" s:downloadUrl: https://raw.githubusercontent.com/Barski-lab/workflows/master/workflows/allele-vcf-rnaseq-pe.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: | Allele specific RNA-Seq (using vcf) paired-end workflow