cwl/annotation/snpeff-bcftools-annotate.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: Run SnpEff on given VCF and use bcftools to annotate with dbSNP and gnomAD
   8 requirements:
   9   ShellCommandRequirement: {}
  10 hints:
  11   DockerRequirement:
  12     dockerPull: snpeff4.3t
  13   ResourceRequirement:
  14     coresMin: 2
  15     ramMin: 20000
  16     tmpdirMin: 16000
  17 inputs:
  18   vcf:
  19     type: File
  20     label: Input VCF
  21   sample:
  22     type: string
  23     label: Sample name
  24   snpeffdatadir:
  25     type: Directory
  26     label: Database directory for SnpEff
  27   genomeversion:
  28     type: string
  29     label: Genome version
  30   dbsnp:
  31     type: File
  32     label: dbSNP BCF
  33     secondaryFiles: [.csi]
  34   gnomad:
  35     type: File
  36     label: gnomAD BCF
  37     secondaryFiles: [.csi]
  38 outputs:
  39   annotatedvcf:
  40     type: File
  41     label: Annotated VCF
  42     outputBinding:
  43       glob: "*_snpeff_dbsnp_gnomad.vcf.gz"
  44     secondaryFiles: [.tbi]
  45 baseCommand: [java]
  46 arguments:
  47   - -Xmx$(runtime.ram)m
  48   - prefix: "-jar"
  49     valueFrom: "/snpEff/snpEff.jar"
  50   - prefix: "-dataDir"
  51     valueFrom: $(inputs.snpeffdatadir)
  52   - $(inputs.genomeversion)
  53   - $(inputs.vcf)
  54   - shellQuote: False
  55     valueFrom: "|"
  56   - "bgzip"
  57   - "-c"
  58   - shellQuote: False
  59     valueFrom: ">"
  60   - $(inputs.sample)_snpeff.vcf.gz
  61   - shellQuote: False
  62     valueFrom: "&&"
  63   - "tabix"
  64   - $(inputs.sample)_snpeff.vcf.gz
  65   - shellQuote: False
  66     valueFrom: "&&"
  67   - "bcftools"
  68   - "annotate"
  69   - prefix: "--annotations"
  70     valueFrom: $(inputs.dbsnp)
  71   - prefix: "--columns"
  72     valueFrom: "=ID"
  73   - $(inputs.sample)_snpeff.vcf.gz
  74   - "-Oz"
  75   - prefix: "-o"
  76     valueFrom: $(inputs.sample)_snpeff_dbsnp.vcf.gz
  77   - shellQuote: False
  78     valueFrom: "&&"
  79   - "tabix"
  80   - $(inputs.sample)_snpeff_dbsnp.vcf.gz
  81   - shellQuote: False
  82     valueFrom: "&&"
  83   - "bcftools"
  84   - "annotate"
  85   - prefix: "--annotations"
  86     valueFrom: $(inputs.gnomad)
  87   - prefix: "--columns"
  88     valueFrom: "INFO/AC,INFO/AN,INFO/AF,INFO/AF_afr,INFO/AF_amr,INFO/AF_asj,INFO/AF_eas,INFO/AF_fin,INFO/AF_nfe,INFO/AF_oth"
  89   - $(inputs.sample)_snpeff_dbsnp.vcf.gz
  90   - "-Oz"
  91   - prefix: "-o"
  92     valueFrom: $(inputs.sample)_snpeff_dbsnp_gnomad.vcf.gz
  93   - shellQuote: False
  94     valueFrom: "&&"
  95   - "tabix"
  96   - $(inputs.sample)_snpeff_dbsnp_gnomad.vcf.gz
  97   - shellQuote: False
  98     valueFrom: "&&"
  99   - "rm"
 100   - $(inputs.sample)_snpeff.vcf.gz
 101   - $(inputs.sample)_snpeff.vcf.gz.tbi
 102   - $(inputs.sample)_snpeff_dbsnp.vcf.gz
 103   - $(inputs.sample)_snpeff_dbsnp.vcf.gz.tbi