WGS-processing/cwl/helper/mark-duplicates.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Mark duplicates using GATK (Picard)
   4
   5 requirements:
   6   DockerRequirement:
   7     dockerPull: broadinstitute/gatk:4.1.7.0
   8
   9 hints:
  10   ResourceRequirement:
  11     ramMin: 20000
  12     coresMin: 4
  13   arv:RuntimeConstraints:
  14     outputDirType: keep_output_dir
  15   SoftwareRequirement:
  16     packages:
  17       GATK:
  18         specs: [ "https://identifiers.org/rrid/RRID:SCR_001876" ]
  19         version: [ "4.1.7" ]
  20
  21 inputs:
  22   bam:
  23     type: File
  24     format: edam:format_2572 # BAM
  25     label: Sorted BAM
  26
  27 outputs:
  28   dupbam:
  29     type: File
  30     format: edam:format_2572 # BAM
  31     label: Sorted BAM with labeled duplicates
  32     outputBinding:
  33       glob: "*.bam"
  34   dupmetrics:
  35     type: File
  36     label: Duplication metrics file
  37     outputBinding:
  38       glob: "*.txt"
  39
  40 baseCommand: /gatk/gatk
  41
  42 arguments:
  43   - "--java-options"
  44   - "-Xmx8G"
  45   - MarkDuplicates
  46   - prefix: "-I"
  47     valueFrom: $(inputs.bam.path)
  48   - prefix: "-O"
  49     valueFrom: marked_dups$(inputs.bam.basename)
  50   - prefix: "-M"
  51     valueFrom: "metrics.txt"
  52
  53 s:codeRepository: https://github.com/arvados/arvados-tutorial
  54 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  55
  56 $namespaces:
  57  s: https://schema.org/
  58  edam: http://edamontology.org/
  59  arv: "http://arvados.org/cwl#"
  60  cwltool: "http://commonwl.org/cwltool#"
  61
  62 #$schemas:
  63 # - https://schema.org/version/latest/schema.rdf
  64 # - http://edamontology.org/EDAM_1.18.owl