name: last_lastal
description: Find suitable score parameters for sequence alignment
keywords:
  - LAST
  - align
  - fastq
  - fasta
tools:
  - last:
      description: LAST finds & aligns related regions of sequences.
      homepage: https://gitlab.com/mcfrith/last
      documentation: https://gitlab.com/mcfrith/last/-/blob/main/doc/last-train.rst
      tool_dev_url: https://gitlab.com/mcfrith/last
      doi: ""
      licence: ['GPL v3-or-later']

input:
  - index:
      type: directory
      description: Directory containing the files of the LAST index
      pattern: "lastdb/"
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fastx:
      type: file
      description: FASTA/FASTQ file
      pattern: "*.{fasta,fastq}"
  - param_file:
      type: file
      description: Trained parameter file
      pattern: "*.par"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - version:
      type: file
      description: File containing software version
      pattern: "versions.yml"
  - maf:
      type: file
      description: Gzipped MAF (Multiple Alignment Format) file
      pattern: "*.{maf.gz}"

authors:
  - "@charles-plessy"