Description

A module to create esm2 embeddings of antibody (BCR) amino acid sequences using amulety.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

tsv{:bash}

:file

TSV with BCR/TCR nucleotide sequences in AIRR rearrangement format

*.{tsv}

chain{:bash}

:string

The chain to use for the embeddings. Can be either ‘H’ (heavy) or ‘HL’ (heavy + light, for single-cell data).

Output

name:type
description
pattern

embedding{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.tsv{:bash}

:file

TSV with esm2 embeddings.

*.tsv

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

amulety
GPL v3

Python package to create embeddings of BCR and TCR amino acid sequences.

amulety.readthedocs.io/en/latest https://github.com/immcantation/amulety 10.1101/2025.03.21.644583
included in
airrflow
maintainer
Github user ggabernet
get in touch
Ask a question on Slack Open an issue on GitHub