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

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Generate recalibration table for BQSR
   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   knownsites1:
  45     type: File
  46     format: edam:format_3016 # VCF
  47     label: VCF of known SNPS sites for BQSR
  48     secondaryFiles:
  49       - .idx
  50   knownsites2:
  51     type: File
  52     format: edam:format_3016 # VCF
  53     label: VCF of known indel sites for BQSR
  54     secondaryFiles:
  55       - .tbi
  56   intervallist:
  57     type: File
  58     label: Scatter intervals file
  59
  60 outputs:
  61   recaltable:
  62     type: File
  63     label: Recalibration table for given interval
  64     outputBinding:
  65       glob: "*.table"
  66
  67 baseCommand: /gatk/gatk
  68
  69 arguments:
  70   - "--java-options"
  71   - "-Xmx4G"
  72   - BaseRecalibrator
  73   - prefix: "-R"
  74     valueFrom: $(inputs.reference)
  75   - prefix: "-I"
  76     valueFrom: $(inputs.bam)
  77   - prefix: "--known-sites"
  78     valueFrom: $(inputs.knownsites1)
  79   - prefix: "--known-sites"
  80     valueFrom: $(inputs.knownsites2)
  81   - prefix: "-L"
  82     valueFrom: $(inputs.intervallist)
  83   - prefix: "-O"
  84     valueFrom: $(inputs.sample)_recal_data.table
  85
  86 s:codeRepository: https://github.com/arvados/arvados-tutorial
  87 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  88
  89 $namespaces:
  90  s: https://schema.org/
  91  edam: http://edamontology.org/
  92  arv: "http://arvados.org/cwl#"
  93  cwltool: "http://commonwl.org/cwltool#"
  94
  95 #$schemas:
  96 # - https://schema.org/version/latest/schema.rdf
  97 # - http://edamontology.org/EDAM_1.18.owl