picard_mergevcfs.cwl

cwlVersion: v1.0
class: CommandLineTool
id: picard_mergevcfs
doc: |-
  This tool merges many VCFs into a single VCF.
  The following programs are run in this tool:
    - picard MergeVcfs
requirements:
  - class: InlineJavascriptRequirement
  - class: ShellCommandRequirement
  - class: ResourceRequirement
    ramMin: 3000
    coresMin: 4
  - class: DockerRequirement
    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
baseCommand: [ "/bin/bash", "-c" ]
arguments:
  - position: 1
    shellQuote: false
    valueFrom: >-
      'set -eo pipefail;
      java -Xms2000m -jar /picard.jar MergeVcfs
      OUTPUT=/dev/stdout
      CREATE_INDEX=false
      VERBOSITY=WARNING
  - position: 3
    shellQuote: false
    valueFrom: >-
      | bgzip -c -@ 4 > $(inputs.output_vcf_basename).g.vcf.gz && tabix -p vcf $(inputs.output_vcf_basename).g.vcf.gz'
inputs:
  input_vcf:
    type:
      type: array
      items: File
      inputBinding:
        prefix: "INPUT="
        separate: false
        position: 2
    inputBinding: { position: 2, shellQuote: false}
    secondaryFiles: [.tbi]
  output_vcf_basename: { type: string, doc: "String to be used as the base filename for the output" }
outputs:
  output: { type: File, outputBinding: { glob: '*.vcf.gz' }, secondaryFiles: [.tbi] }