WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Apply base quality score recalibration
   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   bam:
  24     type: File
  25     format: edam:format_2572 # BAM
  26     label: Indexed sorted BAM with labeled duplicates
  27     secondaryFiles:
  28       - .bai
  29   reference:
  30     type: File
  31     format: edam:format_1929 # FASTA
  32     label: Reference genome
  33     secondaryFiles:
  34       - .amb
  35       - .ann
  36       - .bwt
  37       - .pac
  38       - .sa
  39       - .fai
  40       - ^.dict
  41   sample:
  42     type: string
  43     label: Sample Name
  44   recaltable:
  45     type: File
  46     label: Recalibration table
  47   intervallist:
  48     type: File
  49     label: Scatter intervals file
  50
  51 outputs:
  52   recalbam:
  53     type: File
  54     format: edam:format_2572 # BAM
  55     label: Recalibrated BAM for given interval
  56     secondaryFiles:
  57       - .bai
  58     outputBinding:
  59       glob: "*nodups_BQSR.bam"
  60
  61 baseCommand: /gatk/gatk
  62
  63 arguments:
  64   - "--java-options"
  65   - "-Xmx4G"
  66   - ApplyBQSR
  67   - prefix: "-R"
  68     valueFrom: $(inputs.reference)
  69   - prefix: "-I"
  70     valueFrom: $(inputs.bam)
  71   - prefix: "--bqsr-recal-file"
  72     valueFrom: $(inputs.recaltable)
  73   - prefix: "-L"
  74     valueFrom: $(inputs.intervallist)
  75   - prefix: "-O"
  76     valueFrom: $(inputs.sample)nodups_BQSR.bam
  77
  78 s:codeRepository: https://github.com/arvados/arvados-tutorial
  79 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  80
  81 $namespaces:
  82  s: https://schema.org/
  83  edam: http://edamontology.org/
  84  arv: "http://arvados.org/cwl#"
  85  cwltool: "http://commonwl.org/cwltool#"
  86
  87 #$schemas:
  88 # - https://schema.org/version/latest/schema.rdf
  89 # - http://edamontology.org/EDAM_1.18.owl