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

   1 cwlVersion: v1.1
   2 class: Workflow
   3 label: Variant calling workflow for given interval
   4
   5 requirements:
   6   - class: SubworkflowFeatureRequirement
   7
   8 inputs:
   9   bam:
  10     type: File
  11     format: edam:format_2572 # BAM
  12     label: Indexed sorted BAM with labeled duplicates
  13     secondaryFiles:
  14       - .bai
  15   reference:
  16     type: File
  17     format: edam:format_1929 # FASTA
  18     label: Reference genome
  19     secondaryFiles:
  20       - .amb
  21       - .ann
  22       - .bwt
  23       - .pac
  24       - .sa
  25       - .fai
  26       - ^.dict
  27   sample:
  28     type: string
  29     label: Sample Name
  30   knownsites:
  31     type: File
  32     format: edam:format_3016 # VCF
  33     label: VCF of known polymorphic sites for BQSR
  34     secondaryFiles:
  35       - .tbi
  36   intervallist:
  37     type: File
  38     label: Scatter intervals file
  39
  40 outputs:
  41   gvcf:
  42     type: File
  43     format: edam:format_3016 # GVCF
  44     label: Given interval filtered GVCF
  45     outputSource: selectvariants/filteredgvcf
  46
  47 steps:
  48   basecalibrator:
  49     run: gatk-baserecalibrator-with-interval.cwl
  50     in:
  51       bam: bam
  52       reference: reference
  53       sample: sample
  54       knownsites: knownsites
  55       intervallist: intervallist
  56     out: [recaltable]
  57   applyBQSR:
  58     run: gatk-applyBSQR-with-interval.cwl
  59     in:
  60       reference: reference
  61       bam: bam
  62       sample: sample
  63       intervallist: intervallist
  64       recaltable: basecalibrator/recaltable
  65     out: [recalbam]
  66   haplotypecaller:
  67     run: gatk-haplotypecaller-with-interval.cwl
  68     in:
  69       reference: reference
  70       bam: applyBQSR/recalbam
  71       sample: sample
  72       intervallist: intervallist
  73     out: [gvcf]
  74   selectvariants:
  75     run: gatk-selectvariants.cwl
  76     in:
  77       gvcf: haplotypecaller/gvcf
  78       reference: reference
  79       sample: sample
  80     out: [filteredgvcf]
  81
  82 s:codeRepository: https://github.com/arvados/arvados-tutorial
  83 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  84
  85 $namespaces:
  86  s: https://schema.org/
  87  edam: http://edamontology.org/
  88
  89 $schemas:
  90  - https://schema.org/version/latest/schema.rdf
  91  - http://edamontology.org/EDAM_1.18.owl