#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow label: "regtools workflow" requirements: - class: ScatterFeatureRequirement inputs: rna_tumor_bam: type: File doc: RNAseq aligned tumor bam reference: type: File doc: Fasta file containing the reference corresponding to the bam files transcriptome: type: File doc: GTF file giving the transcriptome used to annotate against variants: type: File doc: VCF file providing somatic variant calls e: type: string[]? default: ["2", "5"] i: type: string[]? default: ["3", "50"] outputs: cis_splice_effects_identify: type: File[] outputSource: cis_splice_effects/aberrant_splice_junctions cis_splice_effects_identify_v2: type: File outputSource: cis_splice_effects_v2/aberrant_splice_junctions cis_splice_effects_identify_v3: type: File outputSource: cis_splice_effects_v3/aberrant_splice_junctions junctions_extract_out: type: File outputSource: junctions_extract/junctions junctions_annotate_out: type: File outputSource: junctions_annotate/junctions_annotated steps: cis_splice_effects: scatter: [ e, i ] scatterMethod: dotproduct run: cis_splice_effects.cwl in: e: e i: i variants: variants bam: rna_tumor_bam ref: reference gtf: transcriptome out: [ aberrant_splice_junctions ] cis_splice_effects_v2: run: cis_splice_effects_v2.cwl in: variants: variants bam: rna_tumor_bam ref: reference gtf: transcriptome out: [ aberrant_splice_junctions ] cis_splice_effects_v3: run: cis_splice_effects_v3.cwl in: variants: variants bam: rna_tumor_bam ref: reference gtf: transcriptome out: [ aberrant_splice_junctions ] junctions_extract: run: junctions_extract.cwl in: bam: rna_tumor_bam out: [ junctions ] junctions_annotate: run: junctions_annotate.cwl in: junctions: junctions_extract/junctions ref: reference gtf: transcriptome out: [ junctions_annotated ]