#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow inputs: fastqc_reports: type: { type: array, items: { type: array, items: File } } trim_reports: type: { type: array, items: { type: array, items: File } } bams_markduplicates: File[] raw_variants: File[] bams_recalibrated: File[] outputs: fastqc_reports_dir: type: Directory outputSource: org_fastqc_reports/outdir trim_reports_dir: type: Directory outputSource: org_trim_reports/outdir bams_markduplicates_dir: type: Directory outputSource: org_bams_markduplicates/outdir raw_variants_dir: type: Directory outputSource: org_raw_variants/outdir bams_recalibrated_dir: type: Directory outputSource: org_bams_recalibrated/outdir steps: org_fastqc_reports: run: ../tools/file-pairs-to-directory.cwl in: name: default: 'fastqc-reports' file_pairs: fastqc_reports out: - outdir org_trim_reports: run: ../tools/file-pairs-to-directory.cwl in: name: default: 'trim-reports' file_pairs: trim_reports out: - outdir org_bams_markduplicates: run: ../tools/files-to-directory.cwl in: name: default: 'bams-markduplicates' files: bams_markduplicates out: - outdir org_raw_variants: run: ../tools/files-to-directory.cwl in: name: default: 'gvcfs' files: raw_variants out: - outdir org_bams_recalibrated: run: ../tools/files-to-directory.cwl in: name: default: 'bams-recalibrated' files: bams_recalibrated out: - outdir