WGS-processing/cwl/helper/gvcf-to-vcf.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Convert GVCF to VCF
   4
   5 requirements:
   6   - class: DockerRequirement
   7     dockerPull: curii/clinvar-report
   8   - class: ShellCommandRequirement
   9
  10 hints:
  11   ResourceRequirement:
  12     ramMin: 10000
  13     coresMin: 4
  14   SoftwareRequirement:
  15     packages:
  16       BCFtools:
  17         specs: [ "https://identifiers.org/rrid/RRID:SCR_005227" ]
  18         version: [ "1.10.2" ]
  19       HTSlib:
  20         version: [ "1.10.2" ]
  21
  22 inputs:
  23   sample:
  24     type: string
  25     label: Sample Name
  26   gvcf:
  27     type: File
  28     format: edam:format_3016 # GVCF
  29     label: GVCF generated from GATK
  30
  31 outputs:
  32   vcf:
  33     type: File
  34     format: edam:format_3016 # VCF
  35     label: VCF extracted from GVCF
  36     outputBinding:
  37       glob: "*.vcf.gz"
  38     secondaryFiles: [.tbi]
  39
  40 arguments:
  41   - bcftools
  42   - view
  43   - prefix: "--min-ac"
  44     valueFrom: "1"
  45   - $(inputs.gvcf.path)
  46   - prefix: "-i"
  47     valueFrom: "AVG(GQ)>20"
  48   - valueFrom: "-Ov"
  49   - prefix: "-o"
  50     valueFrom: $(inputs.sample).vcf
  51   - {valueFrom: '&&', shellQuote: false}
  52   - bgzip
  53   - valueFrom: $(inputs.sample).vcf
  54   - {valueFrom: '&&', shellQuote: false}
  55   - tabix
  56   - valueFrom: $(inputs.sample).vcf.gz
  57
  58 s:codeRepository: https://github.com/arvados/arvados-tutorial
  59 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  60
  61 $namespaces:
  62  s: https://schema.org/
  63  edam: http://edamontology.org/
  64
  65 $schemas:
  66  - https://schema.org/version/latest/schema.rdf
  67  - http://edamontology.org/EDAM_1.18.owl