---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "branch_hits_fasta"
description: Check if there are hmmsearch matches for sequences and if so, assign them to the respective hit family file, else put them in a fasta.gz file.
keywords:
  - chunking
  - clusters
  - fasta
tools:
  - "branch_hits_fasta":
      description: "Check if there are hmmsearch matches for sequences and if so, assign them to the respective hit family file, else put them in a fasta.gz file."
      homepage: "https://github.com/nf-core/proteinfamilies/tree/dev/modules/local/branch_hits_fasta/"
      documentation: "https://github.com/nf-core/proteinfamilies/tree/dev/modules/local/branch_hits_fasta/"
      tool_dev_url: "https://github.com/nf-core/proteinfamilies/tree/dev/modules/local/branch_hits_fasta/"
      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 ]`
    - fasta:
        type: file
        description: Input amino acid fasta file.
        pattern: "*.{fasta,faa,fa,fasta.gz,faa.gz,fa.gz}"
  - - 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 input sequences against existing family HMM hits.
        pattern: "*.domtbl.gz"
  - - length_threshold:
        type: float
        description: The minimum HMM query hit length percentage to consider for a family hit.
output:
  hits:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
    - hits/*:
        type: file
        description: List of fasta files containing sequences that had HMM hits across families -one file per family.
        pattern: "hits/*.fasta"
  non_hit_fasta:
    - - meta2:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
    - .fasta.gz:
        type: file
        description: Updated compressed input fasta file containing non-hit sequences, to go through the basic family generation workflow.
        pattern: "*.fasta.gz"
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
  - "@vagkaratzas"
maintainers:
  - "@vagkaratzas"
