name: nucmer
description: NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences.
keywords:
  - align
  - nucleotide
tools:
  - nucmer:
      description: NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences.
      homepage: http://mummer.sourceforge.net/
      documentation: http://mummer.sourceforge.net/
      tool_dev_url: http://mummer.sourceforge.net/
      doi: "https://doi.org/10.1186/gb-2004-5-2-r12"
      licence: ['The Artistic License']

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

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"
  - delta:
      type: file
      description: File containing coordinates of matches between reference and query
  - coords:
      type: file
      description: NUCmer1.1 coords output file
      pattern: "*.{coords}"

authors:
  - "@sateeshperi"
  - "@mjcipriano"