name: graphmap2_align
description: A versatile pairwise aligner for genomic and spliced nucleotide sequences
keywords:
  - align
  - fasta
  - fastq
  - genome
  - reference
tools:
  - graphmap2:
      description: |
        A versatile pairwise aligner for genomic and spliced nucleotide sequences.
      homepage: https://github.com/lbcb-sci/graphmap2
      documentation: https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads
      licence: ["MIT"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fastq:
      type: file
      description: |
        List of input FASTQ files
        and paired-end data, respectively.
  - fasta:
      type: file
      description: |
        Reference database in FASTA format.
  - index:
      type: file
      description: |
        FASTA index in gmidx.
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - sam:
      type: file
      description: Alignment in SAM format
      pattern: "*.sam"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@yuukiiwa"
  - "@drpatelh"