name: "bcftools_convert"
description: Converts certain output formats to VCF
keywords:
  - bcftools
  - convert
  - vcf
  - gvcf
tools:
  - "bcftools":
      description: "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.  Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations."
      homepage: "https://samtools.github.io/bcftools/bcftools.html"
      documentation: "https://samtools.github.io/bcftools/bcftools.html#convert"
      tool_dev_url: "https://github.com/samtools/bcftools"
      doi: "https://doi.org/10.1093/gigascience/giab008"
      licence: "['GPL']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - input:
      type: file
      description: |
        The input format. Each format needs a seperate parameter to be specified in the `args`:
        - GEN/SAMPLE file: `--gensample2vcf`
        - gVCF file: `--gvcf2vcf`
        - HAP/SAMPLE file: `--hapsample2vcf`
        - HAP/LEGEND/SAMPLE file: `--haplegendsample2vcf`
        - TSV file: `--tsv2vcf`
      pattern: "*.{gen,sample,g.vcf,hap,legend}{.gz,}"
  - input_index:
      type: file
      description: (Optional) The index for the input files, if needed
      pattern: "*.bed"
  - bed:
      type: file
      description: (Optional) The BED file containing the regions for the VCF file
      pattern: "*.bed"
  - fasta:
      type: file
      description: (Optional) The reference fasta, only needed for gVCF conversion
      pattern: "*.{fa,fasta}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - vcf_gz:
      type: file
      description: VCF merged output file (bgzipped) => when `--output-type z` is used
      pattern: "*.vcf.gz"
  - vcf:
      type: file
      description: VCF merged output file => when `--output-type v` is used
      pattern: "*.vcf"
  - bcf_gz:
      type: file
      description: BCF merged output file (bgzipped) => when `--output-type b` is used
      pattern: "*.bcf.gz"
  - bcf:
      type: file
      description: BCF merged output file => when `--output-type u` is used
      pattern: "*.bcf"

authors:
  - "@nvnieuwk"