name: bcftools_view
description: View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
keywords:
    - variant calling
    - view
    - bcftools
    - VCF

tools:
    - view:
        description: |
          View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
        homepage: http://samtools.github.io/bcftools/bcftools.html
        documentation: http://www.htslib.org/doc/bcftools.html
        doi: 10.1093/bioinformatics/btp352
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 inspected.
          e.g. 'file.vcf'
    - index:
        type: file
        description: |
          The tab index for the VCF file to be inspected.
          e.g. 'file.tbi'
    - regions:
        type: file
        description: |
          Optionally, restrict the operation to regions listed in this file.
          e.g. 'file.vcf'
    - targets:
        type: file
        description: |
          Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
          e.g. 'file.vcf'
    - samples:
        type: file
        description: |
          Optional, file of sample names to be included or excluded.
          e.g. 'file.tsv'
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"