name: "hmmer_eslreformat"
description: reformats sequence files, see HMMER documentation for details. The module requires that the format is specified in ext.args in a config file, and that this comes last. See the tools help for possible values.
keywords:
  - sort
tools:
  - "hmmer":
      description: "Biosequence analysis using profile hidden Markov models"
      homepage: http://hmmer.org/
      documentation: http://hmmer.org/documentation.html

      doi: "10.1371/journal.pcbi.1002195"
      licence: ["BSD-3-Clause"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - seqfile:
      type: file
      description: Sequences, aligned or not, in any supported format
      pattern: "*"

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"
  - seqreformated:
      type: file
      description: Reformated sequence file
      pattern: "*.*.gz"

authors:
  - "@erikrikarddaniel"
