cwl/imputation/beagle.cwl

   1 # Copyright (C) The Lightning Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 cwlVersion: v1.1
   6 class: CommandLineTool
   7 requirements:
   8   ShellCommandRequirement: {}
   9 hints:
  10   DockerRequirement:
  11     dockerPull: beagle5.4
  12   ResourceRequirement:
  13     coresMin: 2
  14     ramMin: 10000
  15 inputs:
  16   sample: string
  17   chr: string
  18   ref: File
  19   map: File
  20   vcf:
  21     type: File
  22     secondaryFiles: [.tbi]
  23 outputs:
  24   rawimputedvcf:
  25     type: File
  26     outputBinding:
  27       glob: "*.vcf.gz"
  28     secondaryFiles: [.tbi]
  29 baseCommand: [bcftools, view]
  30 arguments:
  31   - $(inputs.vcf)
  32   - prefix: "--regions"
  33     valueFrom: $(inputs.chr)
  34   - "-Oz"
  35   - prefix: "-o"
  36     valueFrom: $(inputs.sample)_$(inputs.chr).vcf.gz
  37   - shellQuote: false
  38     valueFrom: "&&"
  39   - "java"
  40   - -Xms$(runtime.ram)m
  41   - prefix: "-jar"
  42     valueFrom: "/beagle.05May22.33a.jar"
  43   - prefix: "ref="
  44     separate: false
  45     valueFrom: $(inputs.ref)
  46   - prefix: "map="
  47     separate: false
  48     valueFrom: $(inputs.map)
  49   - prefix: "gt="
  50     separate: false
  51     valueFrom: $(inputs.sample)_$(inputs.chr).vcf.gz
  52   - prefix: "out="
  53     separate: false
  54     valueFrom: $(inputs.sample)_rawimputed_$(inputs.chr)
  55   - prefix: "nthreads="
  56     separate: false
  57     valueFrom: $(runtime.cores)
  58   - shellQuote: false
  59     valueFrom: "&&"
  60   - "tabix"
  61   - $(inputs.sample)_rawimputed_$(inputs.chr).vcf.gz
  62   - shellQuote: false
  63     valueFrom: "&&"
  64   - "rm"
  65   - $(inputs.sample)_$(inputs.chr).vcf.gz