name: mash_dist
description: Calculate Mash distances between reference and query seqeunces
keywords:
  - mash/dist
tools:
  - mash:
      description: Fast sequence distance estimator that uses MinHash
      homepage: https://github.com/marbl/Mash
      documentation: https://mash.readthedocs.io/en/latest/sketches.html
      tool_dev_url: https://github.com/marbl/Mash
      doi: "10.1186/s13059-016-0997-x"
      licence: ['https://github.com/marbl/Mash/blob/master/LICENSE.txt']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reference:
      type: file
      description: FASTA, FASTQ or Mash sketch
      pattern: "*.{fasta,fasta.gz,fastq,fastq.gz,msh}"
  - query:
      type: file
      description: FASTA, FASTQ or Mash sketch
      pattern: "*.{fasta,fasta.gz,fastq,fastq.gz,msh}"

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"
  - dist:
      type: file
      description: The results from mash dist
      pattern: "*.txt"

authors:
  - "@rpetit3"