#!/usr/bin/env cwl-runner # # Author: jeltje.van.baren@gmail.com class: Workflow cwlVersion: "v1.0" doc: | A workflow for running MuSe, MuTect, SomaticSniper, and Pindel. See [the github repository](https://github.com/BD2KGenomics/dockstore_workflow_snps) for details. requirements: - class: MultipleInputFeatureRequirement - class: StepInputExpressionRequirement - class: InlineJavascriptRequirement inputs: - id: NORMAL_BAM type: File secondaryFiles: - .bai - id: TUMOR_BAM type: File secondaryFiles: - .bai - id: COSMIC_VCF type: File secondaryFiles: - .tbi - id: DBSNP_VCF type: File secondaryFiles: - .tbi - id: CENTROMERE_BED type: File - id: CPUS type: int - id: MODE type: string - id: GENO_FA type: File secondaryFiles: - .fai - ^.dict outputs: OUTPUT: type: File outputSource: tar/tarredfile steps: muse: run: ./muse.cwl in: mode: MODE reference: GENO_FA normal: NORMAL_BAM tumor: TUMOR_BAM known: DBSNP_VCF ncpus: CPUS out: [mutations] muse_filter: run: ./muse_filter.cwl in: vcf: muse/mutations out: [output_vcf] mutect: run: ./mutect.cwl in: reference: GENO_FA normal: NORMAL_BAM tumor: TUMOR_BAM dbsnp: DBSNP_VCF cosmic: COSMIC_VCF ncpus: CPUS out: [mutations] pindel: run: ./pindel.cwl in: reference: GENO_FA normal: NORMAL_BAM tumor: TUMOR_BAM procs: CPUS centromere: CENTROMERE_BED out: [somatic_vcf] somaticsniper: run: ./somatic_sniper.cwl in: reference: GENO_FA normal: NORMAL_BAM tumor: TUMOR_BAM procs: CPUS out: [mutations] tar: run: tar.cwl in: muse: muse_filter/output_vcf mutect: mutect/mutations pindel: pindel/somatic_vcf somsni: somaticsniper/mutations tarfile: valueFrom: $('vcfs.tgz') out: [tarredfile]