WGS-processing/cwl/helper/gatk-selectvariants.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Filter unused alternates
   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   gvcf:
  24     type: File
  25     format: edam:format_3016 # GVCF
  26     label: GVCF for given interval
  27     secondaryFiles:
  28       - .tbi
  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
  45 outputs:
  46   filteredgvcf:
  47     type: File
  48     format: edam:format_3016 # GVCF
  49     label: Given interval filtered GVCF
  50     outputBinding:
  51       glob: "*g.vcf.gz"
  52
  53 baseCommand: /gatk/gatk
  54
  55 arguments:
  56   - "--java-options"
  57   - "-Xmx4G"
  58   - SelectVariants
  59   - prefix: "-R"
  60     valueFrom: $(inputs.reference)
  61   - prefix: "--remove-unused-alternates"
  62     valueFrom: "true"
  63   - prefix: "-V"
  64     valueFrom: $(inputs.gvcf.path)
  65   - prefix: "-O"
  66     valueFrom: selected$(inputs.gvcf.basename)
  67
  68 s:codeRepository: https://github.com/arvados/arvados-tutorial
  69 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  70
  71 $namespaces:
  72  s: https://schema.org/
  73  edam: http://edamontology.org/
  74  arv: "http://arvados.org/cwl#"
  75  cwltool: "http://commonwl.org/cwltool#"
  76
  77 $schemas:
  78  - https://schema.org/version/latest/schema.rdf
  79  - http://edamontology.org/EDAM_1.18.owl