name: seqkit_replace
description: Use seqkit to find/replace strings within sequences and sequence headers
keywords:
  - seqkit
  - replace
tools:
  - seqkit:
      description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
      homepage: https://bioinf.shenwei.me/seqkit/usage/
      documentation: https://bioinf.shenwei.me/seqkit/usage/
      tool_dev_url: https://github.com/shenwei356/seqkit/
      doi: "10.1371/journal.pone.016396"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fastx:
      type: file
      description: fasta/q file
      pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*"

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"
  - fastx:
      type: file
      description: fasta/q file with replaced values
      pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*"

authors:
  - "@mjcipriano"