name: seqkit_replace
description: Use seqkit to find/replace strings within sequences and sequence headers
keywords:
  - seqkit
  - replace
  - sequence
  - sequence headers
  - fasta
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"
      identifier: biotools:seqkit
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}*"
        ontologies:
          - edam: http://edamontology.org/format_1930 # FASTQ
output:
  fastx:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.fast*":
          type: file
          description: fasta/q file with replaced values
          pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*"
          ontologies:
            - edam: http://edamontology.org/format_1930 # FASTQ
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750 # YAML
authors:
  - "@mjcipriano"
maintainers:
  - "@mjcipriano"
