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'
    - 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: VCF normalized output file
        pattern: "*.{vcf.gz}"
    - versions:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
    - "@abhi18av"