---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "extract_family_reps"
description: From a list of alignment files (Stockholm or fasta format) extract a fasta file with the first sequences of each file, as well as a MultiQC CSV with metadata.
keywords:
  - fasta
  - representative sequences
  - multiqc metadata
tools:
  - "extract_family_reps":
      description: "From a list of alignment files (Stockholm or fasta format) extract a fasta file with the first sequences of each file, as well as a MultiQC CSV with metadata."
      homepage: "https://github.com/nf-core/proteinfamilies/tree/dev/modules/local/extract_family_reps/"
      documentation: "https://github.com/nf-core/proteinfamilies/tree/dev/modules/local/extract_family_reps/"
      tool_dev_url: "https://github.com/nf-core/proteinfamilies/tree/dev/modules/local/extract_family_reps/"
      doi: "10.5281/zenodo.14881993"
      licence: ["MIT"]
      identifier: ""
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1', single_end:false ]`
    - aln:
        type: file
        description: A list of alignment files that will be staged as a directory.
        pattern: "*.{sto.gz,fasta,fasta.gz}"
output:
  fasta:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
    - ${prefix}_reps.faa:
        type: file
        description: a fasta file with all family representative sequences
        pattern: "*_reps.faa"
  map:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
    - ${prefix}_meta_mqc.csv:
        type: file
        description: |
          a MultiQC CSV file with all family representative sequence metadata:
          "Sample Name","Family Id","Size","Representative Length","Representative Id","Sequence"
        pattern: "*_meta_mqc.csv"
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
  - "@vagkaratzas"
maintainers:
  - "@vagkaratzas"
