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

   1 cwlVersion: v1.1
   2 class: Workflow
   3 label: Variant calling workflow for single interval
   4
   5 requirements:
   6   - class: SubworkflowFeatureRequirement
   7
   8 inputs:
   9   bam:
  10     type: File
  11     secondaryFiles:
  12       - .bai
  13   reference:
  14     type: File
  15     secondaryFiles:
  16       - .amb
  17       - .ann
  18       - .bwt
  19       - .pac
  20       - .sa
  21       - .fai
  22       - ^.dict
  23   sample: string
  24   knownsites1:
  25     type: File
  26     secondaryFiles:
  27       - .tbi
  28   intervallist:
  29     type: File
  30
  31 outputs:
  32   gvcf:
  33     type: File
  34     outputSource: selectvariants/filteredgvcf
  35
  36 steps:
  37   basecalibrator:
  38     run: gatk-baserecalibrator-with-interval.cwl
  39     in:
  40       bam: bam
  41       reference: reference
  42       sample: sample
  43       knownsites1: knownsites1
  44       intervallist: intervallist
  45     out: [recaltable]
  46   applyBQSR:
  47     run: gatk-applyBSQR-with-interval.cwl
  48     in:
  49       reference: reference
  50       bam: bam
  51       sample: sample
  52       intervallist: intervallist
  53       recaltable: basecalibrator/recaltable
  54     out: [recalbam]
  55   haplotypecaller:
  56     run: gatk-haplotypecaller-with-interval.cwl
  57     in:
  58       reference: reference
  59       bam: applyBQSR/recalbam
  60       sample: sample
  61       intervallist: intervallist
  62     out: [gvcf]
  63   selectvariants:
  64     run: gatk-selectvariants.cwl
  65     in:
  66       gvcf: haplotypecaller/gvcf
  67       reference: reference
  68       sample: sample
  69     out: [filteredgvcf]
  70
  71 s:codeRepository: https://github.com/arvados/arvados-tutorial
  72 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  73
  74 $namespaces:
  75  s: https://schema.org/
  76  edam: http://edamontology.org/
  77
  78 $schemas:
  79  - https://schema.org/version/latest/schema.rdf
  80  - http://edamontology.org/EDAM_1.18.owl