name: bcftools_annotate
description: Add or remove annotations.
keywords:
  - bcftools
  - annotate
  - vcf
  - remove
  - add
tools:
  - annotate:
      description: Add or remove annotations.
      homepage: http://samtools.github.io/bcftools/bcftools.html
      documentation: https://samtools.github.io/bcftools/bcftools.html#annotate
      doi: 10.1093/bioinformatics/btp352
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - input:
      type: file
      description: Query VCF or BCF file, can be either uncompressed or compressed
  - index:
      type: file
      description: Index of the query VCF or BCF file
  - annotations:
      type: file
      description: Bgzip-compressed file with annotations
  - annotations_index:
      type: file
      description: Index of the annotations file
  - header_lines:
      type: file
      description: Contains lines to append to the output VCF header

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:
      type: file
      description: Compressed annotated VCF file
      pattern: "*{vcf,vcf.gz,bcf,bcf.gz}"

authors:
  - "@projectoriented"
  - "@ramprasadn"
