cwlVersion: v1.1 class: CommandLineTool label: Germline variant calling using GATK with output gvcf requirements: DockerRequirement: dockerPull: broadinstitute/gatk InitialWorkDirRequirement: listing: - $(inputs.bam) hints: ResourceRequirement: ramMin: 10000 coresMin: 4 inputs: bam: type: File secondaryFiles: - .bai reference: type: File secondaryFiles: - .amb - .ann - .bwt - .pac - .sa - .fai - ^.dict sample: string outputs: vcf: type: File outputBinding: glob: "*vcf" arguments: - java - -jar - /gatk/gatk.jar - HaplotypeCaller - -R - $(inputs.reference) - -I - $(inputs.bam) - -O - $(runtime.outdir)/$(inputs.sample).gatk.g.vcf - -ERC - "GVCF"