name: hmmer_hmmalign
description: hmmalign from the HMMER suite aligns a number of sequences to an HMM profile
keywords:
  - alignment
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' ]
  - fasta:
      type: file
      description: Amino acid or nucleotide gzipped compressed fasta file
      pattern: "*.{fna.gz,faa.gz,fasta.gz,fa.gz}"
  - hmm:
      type: file
      description: A gzipped HMM file
      pattern: "*.hmm.gz"

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"
  - sthlm:
      type: file
      description: Multiple alignment in gzipped Stockholm format
      pattern: "*.sthlm.gz"

authors:
  - "@erikrikarddaniel"
  - "@jfy133"
