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   fullintervallist:
  36     type: File
  37     label: Full list of intervals to operate over
  38   sample:
  39     type: string
  40     label: Sample Name
  41   scattercount:
  42     type: string
  43     label: Desired split for variant calling
  44
  45 outputs:
  46   intervalfiles:
  47     type: File[]
  48     label: Scatter intervals files
  49     outputBinding:
  50       glob: "intervalfiles/*.interval_list"
  51
  52 baseCommand: /gatk/gatk
  53
  54 arguments:
  55   - "--java-options"
  56   - "-Xmx4G"
  57   - SplitIntervals
  58   - prefix: "-R"
  59     valueFrom: $(inputs.reference)
  60   - prefix: "-L"
  61     valueFrom: $(inputs.fullintervallist)
  62   - prefix: "--scatter-count"
  63     valueFrom: $(inputs.scattercount)
  64   - prefix: "--subdivision-mode"
  65     valueFrom: "BALANCING_WITHOUT_INTERVAL_SUBDIVISION"
  66   - prefix: "-O"
  67     valueFrom: "intervalfiles"
  68
  69 s:codeRepository: https://github.com/arvados/arvados-tutorial
  70 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  71
  72 $namespaces:
  73  s: https://schema.org/
  74  edam: http://edamontology.org/
  75  arv: "http://arvados.org/cwl#"
  76  cwltool: "http://commonwl.org/cwltool#"
  77
  78 #$schemas:
  79 # - https://schema.org/version/latest/schema.rdf
  80 # - http://edamontology.org/EDAM_1.18.owl