name: "vcf2maf"
description: vcf2maf
keywords:
  - "vcf2maf"
  - annotation
tools:
  - "vcf2maf":
      description: |
        "Convert a VCF into a MAF where each variant is annotated to only one of all possible gene isoforms using vcf2maf. vcf2maf is designed to work with VEP, so it is recommended to have VEP and vcf2maf installed when running this module. Running VEP requires a VEP cache to be present. It is recommended to set the --species and --ncbi-build in ext.args (use the module config). If you wish to skip VEP, add `--inhibit-vep` to ext.args. It may also be necessary to set --tumor-id and --normal-id for correct parsing of the VCF."
      homepage: "https://github.com/mskcc/vcf2maf"
      documentation: "https://github.com/mskcc/vcf2maf"
      tool_dev_url: "https://github.com/mskcc/vcf2maf"
      doi: "10.5281/zenodo.593251"
      licence: "['Apache-2.0']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcf:
      type: file
      description: |
        vcf to convert to MAF format. Must be uncompressed.
  - vep_cache:
      type: file
      description: |
        Path to VEP cache dir. Required for correct running of VEP.

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - maf:
      type: file
      description: MAF file produced from VCF
      pattern: "*.maf"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@adamrtalbot"