cwlVersion: v1.0 class: Workflow requirements: - class: SubworkflowFeatureRequirement - class: StepInputExpressionRequirement - class: InlineJavascriptRequirement - class: MultipleInputFeatureRequirement 'sd:upstream': rnaseq_sample: - "rnaseq-se.cwl" - "rnaseq-pe.cwl" - "rnaseq-se-dutp.cwl" - "rnaseq-pe-dutp.cwl" - "rnaseq-se-dutp-mitochondrial.cwl" - "rnaseq-pe-dutp-mitochondrial.cwl" - "trim-rnaseq-pe.cwl" - "trim-rnaseq-se.cwl" - "trim-rnaseq-pe-dutp.cwl" - "trim-rnaseq-pe-smarter-dutp.cwl" - "trim-rnaseq-se-dutp.cwl" - "trim-quantseq-mrnaseq-se.cwl" inputs: alias: type: string label: "Experiment short name/Alias" sd:preview: position: 1 rpkm_isoforms: type: - "null" - File[] default: null format: "http://edamontology.org/format_3752" label: "RNA-Seq experiments" doc: "CSV/TSV file with RPKM grouped by isoform" 'sd:upstreamSource': "rnaseq_sample/rpkm_isoforms" 'sd:localLabel': true rpkm_genes: type: - "null" - File[] default: null format: "http://edamontology.org/format_3475" label: "RNA-Seq experiments" doc: "CSV/TSV file with RPKM grouped by gene" 'sd:upstreamSource': "rnaseq_sample/rpkm_genes" rpkm_common_tss: type: - "null" - File[] default: null format: "http://edamontology.org/format_3475" label: "RNA-Seq experiments" doc: "CSV/TSV file with RPKM grouped by common TSS" 'sd:upstreamSource': "rnaseq_sample/rpkm_common_tss" sample_names: type: string[] label: "RNA-Seq experiments" doc: | Aliases for RNA-Seq experiments to be used as the names for the reported columns in the merged file. Order corresponds to the rpkm_genes input 'sd:upstreamSource': "rnaseq_sample/alias" group_by: type: - "null" - type: enum symbols: ["isoforms", "genes", "common tss"] default: "genes" label: "Group by" doc: "Grouping method for features: isoforms, genes or common tss" merge_by_columns: type: - "null" - string[] default: ["RefseqId", "GeneId", "Chrom", "TxStart", "TxEnd", "Strand"] label: "Columns to merge experiments by" doc: "Column names to merge feature files by" 'sd:layout': advanced: true outputs: merged_file: type: File label: "Merged feature expression file" format: "http://edamontology.org/format_3475" doc: | Merged by merge_by_columns feature expression file outputSource: feature_merge/merged_file 'sd:visualPlugins': - syncfusiongrid: tab: 'Merged Feature Expression' Title: 'Merged Feature Expression' feature_merge_stdout_log: type: File format: "http://edamontology.org/format_2330" label: "Merging stdout log" doc: "Merging stdout log" outputSource: feature_merge/stdout_log feature_merge_stderr_log: type: File format: "http://edamontology.org/format_2330" label: "Merging stderr log" doc: "Merging stderr log" outputSource: feature_merge/stderr_log steps: feature_merge: run: ../tools/feature-merge.cwl in: feature_files: source: [group_by, rpkm_isoforms, rpkm_genes, rpkm_common_tss] valueFrom: | ${ if (self[0] == "isoforms") { return self[1]; } else if (self[0] == "genes") { return self[2]; } else { return self[3]; } } feature_aliases: sample_names mergeby: merge_by_columns out: - merged_file - 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: "Feature expression merge - combines feature expression from several experiments" label: "Feature expression merge - combines feature expression from several experiments" s:alternateName: "Feature expression merge - combines gene expression from several experiments" s:downloadUrl: https://raw.githubusercontent.com/datirium/workflows/master/workflows/feature-merge.cwl s:codeRepository: https://github.com/datirium/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: | Feature expression merge - combines feature expression from several experiments ========================================================================= Workflows merges RPKM (by default) gene expression from several experiments based on the values from GeneId, Chrom, TxStart, TxEnd and Strand columns (by default). Reported unique columns are renamed based on the experiments names.