cwl/gvcf2fasta/get_bed_varonlyvcf.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 label: Get no call BED and variant only VCF from gVCF
   8 requirements:
   9   ShellCommandRequirement: {}
  10 hints:
  11   DockerRequirement:
  12     dockerPull: vcfutil
  13   ResourceRequirement:
  14     ramMin: 5000
  15     outdirMin: 40000
  16 inputs:
  17   sampleid:
  18     type: string
  19     label: Sample ID
  20   vcf:
  21     type: File
  22     label: Input gVCF
  23   gqcutoff:
  24     type: int
  25     label: GQ (Genotype Quality) cutoff for filtering
  26   genomebed:
  27     type: File
  28     label: Whole genome BED
  29 outputs:
  30   nocallbed:
  31     type: File
  32     label: No call BED of gVCF
  33     outputBinding:
  34       glob: "*_nocall.bed"
  35   varonlyvcf:
  36     type: File
  37     label: Variant only VCF
  38     outputBinding:
  39       glob: "*_varonly.vcf.gz"
  40     secondaryFiles: [.tbi]
  41 baseCommand: /gvcf_regions/gvcf_regions.py
  42 arguments:
  43   - prefix: "--min_GQ"
  44     valueFrom: $(inputs.gqcutoff)
  45   - $(inputs.vcf)
  46   - shellQuote: False
  47     valueFrom: ">"
  48   - $(inputs.sampleid).bed
  49   - shellQuote: False
  50     valueFrom: "&&"
  51   - "bedtools"
  52   - "subtract"
  53   - prefix: "-a"
  54     valueFrom: $(inputs.genomebed)
  55   - prefix: "-b"
  56     valueFrom: $(inputs.sampleid).bed
  57   - shellQuote: False
  58     valueFrom: ">"
  59   - $(inputs.sampleid)_nocall.bed
  60   - shellQuote: False
  61     valueFrom: "&&"
  62   - "bgzip"
  63   - "-dc"
  64   - $(inputs.vcf)
  65   - shellQuote: False
  66     valueFrom: "|"
  67   - "grep"
  68   - "-v"
  69   - "END="
  70   - shellQuote: False
  71     valueFrom: "|"
  72   - "bgzip"
  73   - "-c"
  74   - shellQuote: False
  75     valueFrom: ">"
  76   - $(inputs.sampleid)_varonly.vcf.gz
  77   - shellQuote: False
  78     valueFrom: "&&"
  79   - "tabix"
  80   - $(inputs.sampleid)_varonly.vcf.gz