name: custom_getchromsizes
description: Generates a FASTA file of chromosome sizes and a fasta index file
keywords:
  - fasta
  - chromosome
  - indexing
tools:
  - samtools:
      description: Tools for dealing with SAM, BAM and CRAM files
      homepage: http://www.htslib.org/
      documentation: http://www.htslib.org/doc/samtools.html
      tool_dev_url: https://github.com/samtools/samtools
      doi: 10.1093/bioinformatics/btp352
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: FASTA file
      pattern: "*.{fa,fasta,fna,fas}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - sizes:
      type: file
      description: File containing chromosome lengths
      pattern: "*.{sizes}"
  - 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:
  - "@tamara-hodgetts"
  - "@chris-cheshire"
  - "@muffato"
