name: tabix_bgziptabix
description: bgzip a sorted tab-delimited genome file and then create tabix index
keywords:
  - bgzip
  - compress
  - 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
      pattern: "*.{bed,gff,sam,vcf}"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - gz:
      type: file
      description: Output compressed file
      pattern: "*.{gz}"
  - tbi:
      type: file
      description: tabix index file
      pattern: "*.{gz.tbi}"
  - csi:
      type: file
      description: tabix alternate index file
      pattern: "*.{gz.csi}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@maxulysse"
  - "@DLBPointon"
