# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "seqkit_seq"
description: Transforms sequences (extract ID, filter by length, remove gaps, reverse
  complement...)
keywords:
  - genomics
  - fasta
  - fastq
  - transform
  - filter
  - gaps
  - complement
tools:
  - "seqkit":
      description: "A cross-platform and ultrafast toolkit for FASTA/Q file manipulation"
      homepage: "https://bioinf.shenwei.me/seqkit/"
      documentation: "https://bioinf.shenwei.me/seqkit/usage/"
      tool_dev_url: "https://github.com/shenwei356/seqkit"
      doi: "10.1371/journal.pone.0163962"
      licence: ["MIT"]
      identifier: biotools:seqkit
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1' ]`
    - fastx:
        type: file
        description: Input fasta/fastq file
        pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}"
        ontologies:
          - edam: http://edamontology.org/format_1930 # FASTQ
output:
  fastx:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1' ]`
      - ${prefix}.*:
          type: file
          description: Output fasta/fastq file
          pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}"
          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:
  - "@GallVp"
maintainers:
  - "@GallVp"
