---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "amulety_translate"
description: A module to translate BCR and TCR nucleotide sequences into amino acid sequences using amulety and igblast.
keywords:
  - immunology
  - BCR
  - TCR
  - translation
  - amino acid
  - nucleotide
  - immunoinformatics
tools:
  - "amulety":
      description: "Python package to create embeddings of BCR and TCR amino acid sequences."
      homepage: "https://amulety.readthedocs.io/en/latest/"
      documentation: "https://amulety.readthedocs.io/en/latest/"
      tool_dev_url: "https://github.com/immcantation/amulety"
      doi: "10.1101/2025.03.21.644583"
      licence: ['GPL v3']
  - "igblast":
      description: "A tool for immunoglobulin (IG, BCR) and T cell receptor (TCR) V domain sequences blasting."
      homepage: "https://www.ncbi.nlm.nih.gov/igblast/"
      documentation: "https://ncbi.github.io/igblast/"
      tool_dev_url: "https://github.com/ncbi/igblast"
      doi: "10.1093/nar/gkt382"
      licence: ['United States Government Work']

input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1', single_end:false ]`
    - tsv:
        type: file
        description: TSV with BCR/TCR nucleotide sequences in AIRR rearrangement format
        pattern: "*.{tsv}"
  - - reference_igblast:
        type: file
        description: Built reference databases for igblast

output:
  - repertoire_translated:
    - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1', single_end:false ]`
    - "*_translated.tsv":
        type: file
        description: TSV with BCR/TCR amino acid sequences in AIRR rearrangement format
        pattern: "*.tsv"

  - versions:
    - "versions.yml":
        type: file
        description: File containing software versions
        pattern: "versions.yml"

authors:
  - "@ggabernet"
maintainers:
  - "@ggabernet"
