---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "remove_redundant_seqs"
description: Remove redundant sequences.
keywords:
  - strict clustering
  - representative sequences
  - filtering
tools:
  - "remove_redundant_seqs":
      description: "Keep a fasta with non-redundant amino acid sequences of a family."
      homepage: "https://github.com/nf-core/proteinfamilies/tree/dev/modules/local/remove_redundant_seqs/"
      documentation: "https://github.com/nf-core/proteinfamilies/tree/dev/modules/local/remove_redundant_seqs/"
      tool_dev_url: "https://github.com/nf-core/proteinfamilies/tree/dev/modules/local/remove_redundant_seqs/"
      doi: "10.5281/zenodo.14881993"
      licence: ["MIT"]
      identifier: ""
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing mapping information.
          e.g. `[ id:'sample1', single_end:false ]`
    - clustering:
        type: file
        description: 2-column TSV file mapping sequences to clusters
        pattern: "*.tsv"
  - - meta2:
        type: map
        description: |
          Groovy Map containing mapping information.
          e.g. `[ id:'sample1', single_end:false ]`
    - sequences:
        type: file
        description: fasta file containing amino acid sequences in this family
        pattern: "*.{fa,fa.gz,fasta,fasta.gz}"
output:
  fasta:
    - - meta:
          type: map
          description: |
            Groovy Map containing mapping information
            e.g. `[ id:'sample1', single_end:false ]`
    - ${prefix}_reps.faa:
        type: file
        description: fasta file containing non-redundant, representative sequences
        pattern: "*_reps.faa"
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
  - "@vagkaratzas"
  - "@sillitoe"
maintainers:
  - "@vagkaratzas"
