name: minimap2_align
description: A versatile pairwise aligner for genomic and spliced nucleotide sequences
keywords:
    - align
    - fasta
    - fastq
    - genome
    - paf
    - reference
tools:
    - minimap2:
        description: |
            A versatile pairwise aligner for genomic and spliced nucleotide sequences.
        homepage: https://github.com/lh3/minimap2
        documentation: https://github.com/lh3/minimap2#uguide
input:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - reads:
        type: file
        description: |
            List of input FASTA or FASTQ files of size 1 and 2 for single-end
            and paired-end data, respectively.
    - reference:
        type: file
        description: |
            Reference database in FASTA format.
output:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - paf:
        type: file
        description: Alignment in PAF format
        pattern: "*.paf"
    - version:
        type: file
        description: File containing software version
        pattern: "versions.yml"
authors:
    - "@heuermh"