#!/usr/bin/env cwl-runner class: Workflow cwlVersion: v1.0 inputs: genome: type: string infile: type: File doc: gzip VCF file to annotate outputs: outfile: type: File outputSource: snpeff/output statsfile: type: File outputSource: snpeff/stats genesfile: type: File outputSource: snpeff/genes steps: gunzip: run: gunzip.cwl in: gzipfile: source: infile out: [unzipped_vcf] snpeff: run: snpeff.cwl in: input_vcf: gunzip/unzipped_vcf genome: genome out: [output, stats, genes] doc: | Annotate variants provided in a gziped VCF using SnpEff