name: seqwish_induce
description: Induce a variation graph in GFA format from alignments in PAF format
keywords:
    - induce
    - paf
    - gfa
    - graph
    - variation graph
tools:
    - seqwish:
        description: |
            seqwish implements a lossless conversion from pairwise alignments between
            sequences to a variation graph encoding the sequences and their alignments.
        homepage: https://github.com/ekg/seqwish
        documentation: https://github.com/ekg/seqwish
params:
    - outdir:
        type: string
        description: |
            The pipeline's output directory. By default, the module will
            output files into `$params.outdir/<SOFTWARE>`
    - publish_dir_mode:
        type: string
        description: |
            Value for the Nextflow `publishDir` mode parameter.
            Available: symlink, rellink, link, copy, copyNoFollow, move.
    - enable_conda:
        type: boolean
        description: |
            Run the module with Conda using the software specified
            via the `conda` directive
    - singularity_pull_docker_container:
        type: boolean
        description: |
            Instead of directly downloading Singularity images for use with Singularity,
            force the workflow to pull and convert Docker containers instead.
input:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - paf:
        type: file
        description: PAF file of alignments
        pattern: "*.{paf,paf.gz}"
    - fasta:
        type: file
        description: FASTA file used to generate alignments
        pattern: "*.{fa,fa.gz,fasta,fasta.gz}"

output:
    - meta:
        type: map
        description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
    - gfa:
        type: file
        description: Variation graph in GFA1 format
        pattern: "*.{gfa}"
    - version:
        type: file
        description: File containing software version
        pattern: "*.{version.txt}"
authors:
    - "@heuermh"