---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "identify_redundant_fams"
description: Map families to representative sequences from a CSV, and identify redundancies from hmmsearch domtbl results.
keywords:
  - family redundancy
  - hmmsearch domtbl
  - rep to fam mapping
tools:
  - "identify_redundant_fams":
      description: "Map families to representative sequences from a CSV, and identify redundancies from hmmsearch domtbl results."
      homepage: "https://github.com/nf-core/proteinfamilies/tree/dev/modules/local/identify_redundant_fams/"
      documentation: "https://github.com/nf-core/proteinfamilies/tree/dev/modules/local/identify_redundant_fams/"
      tool_dev_url: "https://github.com/nf-core/proteinfamilies/tree/dev/modules/local/identify_redundant_fams/"
      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 ]`
    - mapping:
        type: file
        description: A CSV file used to map sequences to family IDs.
        pattern: "*.csv"
  - - meta2:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1', single_end:false ]`
    - domtbl:
        type: file
        description: The result of hmmsearch with family rep to family HMM hits.
        pattern: "*.domtbl.gz"
  - - redundancy_length_threshold:
        type: float
        description: The minimum HMM query hit length percentage to consider for redundancy.
  - - similarity_length_threshold:
        type: float
        description: The minimum HMM query hit length percentage to consider for similarity reporting.
output:
  redundant_ids:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1' ]`
      - redundant_fam_ids.txt:
          type: file
          description: A text file with redundant family IDs
          pattern: "redundant_fam_ids.txt"
  similar_ids:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1' ]`
      - similar_fam_ids.txt:
          type: file
          description: A text file with similar family IDs
          pattern: "similar_fam_ids.txt"
  similarities:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1' ]`
      - similarities.csv:
          type: file
          description: A CSV file with pairwise family similarities based on hmmsearch length threshold scores
          pattern: "similarities.csv"
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
  - "@vagkaratzas"
maintainers:
  - "@vagkaratzas"
