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   InitialWorkDirRequirement:
   9     listing:
  10       - $(inputs.bam)
  11
  12 hints:
  13   arv:RuntimeConstraints:
  14     outputDirType: keep_output_dir
  15     keep_cache: 1024
  16   ResourceRequirement:
  17     ramMin: 5000
  18     coresMin: 2
  19   SoftwareRequirement:
  20     packages:
  21       GATK:
  22         specs: [ "https://identifiers.org/rrid/RRID:SCR_001876" ]
  23         version: [ "4.1.7" ]
  24
  25 inputs:
  26   bam:
  27     type: File
  28     format: edam:format_2572 # BAM
  29     label: Indexed sorted BAM with labeled duplicates
  30     secondaryFiles:
  31      - .bai
  32   reference:
  33     type: File
  34     format: edam:format_1929 # FASTA
  35     label: Reference genome
  36     secondaryFiles:
  37       - .amb
  38       - .ann
  39       - .bwt
  40       - .pac
  41       - .sa
  42       - .fai
  43       - ^.dict
  44   sample:
  45     type: string
  46     label: Sample Name
  47   knownsites1:
  48     type: File
  49     format: edam:format_3016 # VCF
  50     label: VCF of known polymorphic sites for BQSR
  51     secondaryFiles:
  52       - .tbi
  53   intervallist:
  54     type: File
  55     label: Scatter intervals file
  56
  57 outputs:
  58   recaltable:
  59     type: File
  60     label: Recalibration table
  61     outputBinding:
  62       glob: "*.table"
  63
  64 baseCommand: /gatk/gatk
  65
  66 arguments:
  67   - "--java-options"
  68   - "-Xmx4G"
  69   - BaseRecalibrator
  70   - prefix: "-R"
  71     valueFrom: $(inputs.reference)
  72   - prefix: "-I"
  73     valueFrom: $(inputs.bam.basename)
  74   - prefix: "--known-sites"
  75     valueFrom: $(inputs.knownsites1)
  76   - prefix: "-L"
  77     valueFrom: $(inputs.intervallist)
  78   - prefix: "-O"
  79     valueFrom: $(inputs.sample)_recal_data.table
  80
  81 s:codeRepository: https://github.com/arvados/arvados-tutorial
  82 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  83
  84 $namespaces:
  85  s: https://schema.org/
  86  edam: http://edamontology.org/
  87  arv: "http://arvados.org/cwl#"
  88  cwltool: "http://commonwl.org/cwltool#"
  89
  90 $schemas:
  91  - https://schema.org/version/latest/schema.rdf
  92  - http://edamontology.org/EDAM_1.18.owl