name: samtools_faidx
description: Index FASTA file
keywords:
  - index
  - fasta
  - faidx
tools:
  - samtools:
      description: |
        SAMtools is a set of utilities for interacting with and post-processing
        short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
        These files are generated as output by short read aligners like BWA.
      homepage: http://www.htslib.org/
      documentation: http://www.htslib.org/doc/samtools.html
      doi: 10.1093/bioinformatics/btp352
      licence: ["MIT"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test' ]
  - fasta:
      type: file
      description: FASTA file
      pattern: "*.{fa,fasta}"
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test' ]
  - fai:
      type: file
      description: FASTA index file
      pattern: "*.{fai}"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fa:
      type: file
      description: FASTA file
      pattern: "*.{fa}"
  - fai:
      type: file
      description: FASTA index file
      pattern: "*.{fai}"
  - gzi:
      type: file
      description: Optional gzip index file for compressed inputs
      pattern: "*.gzi"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@drpatelh"
  - "@ewels"
  - "@phue"
maintainers:
  - "@drpatelh"
  - "@ewels"
  - "@phue"
