cwl/gvcf2fasta/untar-concat-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: Untar, concatenate, and 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   vcftar:
  21     type: File
  22     label: Input gVCF tar
  23   gqcutoff:
  24     type: int
  25     label: GQ (Genotype Quality) cutoff for filtering
  26   genomebed:
  27     type: File
  28     label: Whole genome BED
  29   bashscript:
  30     type: File
  31     label: Script to untar and concatenate vcf tar ball
  32     default:
  33       class: File
  34       location: src/untar-concat.sh
  35 outputs:
  36   nocallbed:
  37     type: File
  38     label: No call BED of gVCF
  39     outputBinding:
  40       glob: "*_nocall.bed"
  41   varonlyvcf:
  42     type: File
  43     label: Variant only VCF
  44     outputBinding:
  45       glob: "*_varonly.vcf.gz"
  46     secondaryFiles: [.tbi]
  47 baseCommand: bash
  48 arguments:
  49   - $(inputs.bashscript)
  50   - $(inputs.sampleid)
  51   - $(inputs.vcftar)
  52   - shellQuote: False
  53     valueFrom: "&&"
  54   - "/gvcf_regions/gvcf_regions.py"
  55   - prefix: "--min_GQ"
  56     valueFrom: $(inputs.gqcutoff)
  57   - $(inputs.sampleid).vcf.gz
  58   - shellQuote: False
  59     valueFrom: ">"
  60   - $(inputs.sampleid).bed
  61   - shellQuote: False
  62     valueFrom: "&&"
  63   - "bedtools"
  64   - "subtract"
  65   - prefix: "-a"
  66     valueFrom: $(inputs.genomebed)
  67   - prefix: "-b"
  68     valueFrom: $(inputs.sampleid).bed
  69   - shellQuote: False
  70     valueFrom: ">"
  71   - $(inputs.sampleid)_nocall.bed
  72   - shellQuote: False
  73     valueFrom: "&&"
  74   - "bgzip"
  75   - "-dc"
  76   - $(inputs.sampleid).vcf.gz
  77   - shellQuote: False
  78     valueFrom: "|"
  79   - "grep"
  80   - "-v"
  81   - "END="
  82   - shellQuote: False
  83     valueFrom: "|"
  84   - "bgzip"
  85   - "-c"
  86   - shellQuote: False
  87     valueFrom: ">"
  88   - $(inputs.sampleid)_varonly.vcf.gz
  89   - shellQuote: False
  90     valueFrom: "&&"
  91   - "tabix"
  92   - $(inputs.sampleid)_varonly.vcf.gz
  93   - shellQuote: False
  94     valueFrom: "&&"
  95   - "rm"
  96   - $(inputs.sampleid).vcf.gz
  97   - $(inputs.sampleid).bed