name: seqtk_rename
description: Rename sequence names in FASTQ or FASTA files.
keywords:
  - rename
tools:
  - seqtk:
      description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk rename command renames sequence names.
      homepage: https://github.com/lh3/seqtk
      documentation: https://docs.csc.fi/apps/seqtk/
      tool_dev_url: https://github.com/lh3/seqtk
      licence: ['MIT']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - sequences:
      type: file
      description: A FASTQ or FASTA file
      pattern: "*.{fastq.gz, fastq, fq, fq.gz, fasta, fastq.gz, fa, fa.gz, fas, fas.gz, fna, fna.gz}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - sequences:
      type: file
      description: FASTQ/FASTA file containing renamed sequences
      pattern: "*.{fastq.gz, fasta.gz}"

authors:
  - "@hseabolt"
  - "@mjcipriano"
  - "@sateeshperi"