---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "amulety_balmpaired"
description: A module to create BALM paired embeddings of antibody (BCR) amino acid sequences using amulety.
keywords:
  - embeddings
  - BCR
  - antibody
  - GPU-accelerated
  - immunoinformatics
  - immunology
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']

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}"
  - - chain:
        type: string
        description: |
          The chain to use for the embeddings. Can be either 'H' (heavy) or 'HL' (heavy + light, for single-cell data).

output:
  - embedding:
    - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1', single_end:false ]`
    - "*.tsv":
        type: file
        description: TSV with BALM paired embeddings.
        pattern: "*.tsv"

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

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