WGS-processing/cwl/helper/gatk-splitintervals.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Create scatter interval files
   4
   5 requirements:
   6   DockerRequirement:
   7     dockerPull: broadinstitute/gatk:4.1.7.0
   8
   9 hints:
  10   arv:RuntimeConstraints:
  11     outputDirType: keep_output_dir
  12     keep_cache: 1024
  13   ResourceRequirement:
  14     ramMin: 5000
  15     coresMin: 2
  16   SoftwareRequirement:
  17     packages:
  18       GATK:
  19         specs: [ "https://identifiers.org/rrid/RRID:SCR_001876" ]
  20         version: [ "4.1.7" ]
  21
  22 inputs:
  23   reference:
  24     type: File
  25     format: edam:format_1929 # FASTA
  26     label: Reference genome
  27     secondaryFiles:
  28       - .amb
  29       - .ann
  30       - .bwt
  31       - .pac
  32       - .sa
  33       - .fai
  34       - ^.dict
  35   sample:
  36     type: string
  37     label: Sample Name
  38   scattercount:
  39     type: string
  40     label: Desired split for variant calling
  41
  42 outputs:
  43   intervalfiles:
  44     type: File[]
  45     label: Scatter intervals files
  46     outputBinding:
  47       glob: "intervalfiles/*.interval_list"
  48
  49 baseCommand: /gatk/gatk
  50
  51 arguments:
  52   - "--java-options"
  53   - "-Xmx4G"
  54   - SplitIntervals
  55   - prefix: "-R"
  56     valueFrom: $(inputs.reference)
  57   - prefix: "--scatter-count"
  58     valueFrom: $(inputs.scattercount)
  59   - prefix: "--subdivision-mode"
  60     valueFrom: "BALANCING_WITHOUT_INTERVAL_SUBDIVISION"
  61   - prefix: "-O"
  62     valueFrom: "intervalfiles"
  63
  64 s:codeRepository: https://github.com/arvados/arvados-tutorial
  65 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  66
  67 $namespaces:
  68  s: https://schema.org/
  69  edam: http://edamontology.org/
  70  arv: "http://arvados.org/cwl#"
  71  cwltool: "http://commonwl.org/cwltool#"
  72
  73 $schemas:
  74  - https://schema.org/version/latest/schema.rdf
  75  - http://edamontology.org/EDAM_1.18.owl