name: bcftools_norm
description: Normalize VCF file
keywords:
  - normalize
  - norm
  - variant calling
  - VCF
tools:
  - norm:
      description: |
        Normalize VCF files.
      homepage: http://samtools.github.io/bcftools/bcftools.html
      documentation: http://www.htslib.org/doc/bcftools.html
      doi: 10.1093/bioinformatics/btp352
      licence: ["MIT"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcf:
      type: file
      description: |
        The vcf file to be normalized
        e.g. 'file1.vcf'
      pattern: "*.{vcf,vcf.gz}"
  - tbi:
      type: file
      description: |
        An optional index of the VCF file (for when the VCF is compressed)
      pattern: "*.vcf.gz.tbi"
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - fasta:
      type: file
      description: FASTA reference file
      pattern: "*.{fasta,fa}"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcf:
      type: file
      description: One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file
      pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@abhi18av"
  - "@ramprasadn"
