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

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Call variants with GATK HaplotypeCaller
   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: 3500
  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: Recalibrated BAM for given interval
  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   intervallist:
  42     type: File
  43     label: Scatter intervals file
  44   sample:
  45     type: string
  46     label: Sample Name
  47
  48 outputs:
  49   gvcf:
  50     type: File
  51     format: edam:format_3016 # GVCF
  52     label: GVCF for given interval
  53     secondaryFiles:
  54       - .tbi
  55     outputBinding:
  56       glob: "*vcf.gz"
  57
  58 baseCommand: /gatk/gatk
  59
  60 arguments:
  61   - "--java-options"
  62   - "-Xmx4G"
  63   - HaplotypeCaller
  64   - prefix: "-R"
  65     valueFrom: $(inputs.reference)
  66   - prefix: "-I"
  67     valueFrom: $(inputs.bam)
  68   - prefix: "-L"
  69     valueFrom: $(inputs.intervallist)
  70   - prefix: "-O"
  71     valueFrom: $(runtime.outdir)/$(inputs.sample)-$(inputs.intervallist.nameroot).gatk.g.vcf.gz
  72   - prefix: "-ERC"
  73     valueFrom: "GVCF"
  74   - prefix: "-GQB"
  75     valueFrom: "5"
  76   - prefix: "-GQB"
  77     valueFrom: "20"
  78   - prefix: "-GQB"
  79     valueFrom: "60"
  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