name: tabix_tabix
description: create tabix index from a sorted bgzip tab-delimited genome file
keywords:
  - index
  - tabix
  - vcf
tools:
  - tabix:
      description: Generic indexer for TAB-delimited genome position files.
      homepage: https://www.htslib.org/doc/tabix.html
      documentation: https://www.htslib.org/doc/tabix.1.html
      doi: 10.1093/bioinformatics/btq671
      licence: ["MIT"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - tab:
      type: file
      description: TAB-delimited genome position file compressed with bgzip
      pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - tbi:
      type: file
      description: tabix index file
      pattern: "*.{tbi}"
  - csi:
      type: file
      description: coordinate sorted index file
      pattern: "*.{csi}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@joseespinosa"
  - "@drpatelh"
  - "@maxulysse"
