---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "chunk_clusters"
description: Chunk an input amino acid sequence file, according to a given clustering TSV and a minimum members' threshold.
keywords:
  - chunking
  - clusters
  - fasta
tools:
  - "chunk_clusters":
      description: "Chunk an input amino acid sequence file, according to a given clustering TSV and a minimum members' threshold"
      homepage: "https://github.com/nf-core/proteinfamilies/tree/dev/modules/local/chunk_clusters/"
      documentation: "https://github.com/nf-core/proteinfamilies/tree/dev/modules/local/chunk_clusters/"
      tool_dev_url: "https://github.com/nf-core/proteinfamilies/tree/dev/modules/local/chunk_clusters/"
      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 ]`
    - clustering:
        type: file
        description: 2-column TSV clustering file (e.g., cluster_rep\tcluster_member).
        pattern: "*.tsv"
  - - meta2:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1', single_end:false ]`
    - sequences:
        type: file
        description: FASTA file containing amino acid sequences.
        pattern: "*.{faa,faa.gz,fa,fa.gz,fasta,fasta.gz}"
  - - size_threshold:
        type: integer
        description: Integer value representing the minimum allowed cluster size to chunk.
output:
  fasta_chunks:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
    - chunked_fasta/*:
        type: file
        description: List of files containing chunked FASTA files produced from the clustering process.
        pattern: "*.faa"
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
  - "@vagkaratzas"
  - "@GiatrasKon"
  - "@marchasapi"
maintainers:
  - "@vagkaratzas"
