Nextflow Registry | nf-core/amulety/embed@0.0.0-0c7146d

nf-core/amulety/embed @ 0.0.0-0c7146d

A module to create embeddings of B-cell receptor (BCR) or T-cell receptor (TCR) amino acid sequences using amulety.

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @ggabernet

Maintainers: @ggabernet

A module to create embeddings of B-cell receptor (BCR) or T-cell receptor (TCR) amino acid sequences using amulety.

Add the following snippet to your workflow script to include this module.

include { AMULETY_EMBED } from 'nf-core/amulety/embed'

MIT License

Process

`Name`	`AMULETY_EMBED`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`tsv` file	TSV with BCR/TCR nucleotide sequences in AIRR rearrangement format `*.{tsv}`

`chain` string	The chain to use for the embeddings. Can be either 'H' (high diversity chain: BCR heavy or TCR beta or delta), 'L' (low diversity chain: BCR light or TCR alpha or gamma) or 'HL'/'LH' (BCR heavy + light, and TCR alpha + beta or gamma + delta).

`model` string	The embedding model to use. Options are detailed on the amulety documentation.

Output 3 channels

#1 embedding tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${task.ext.prefix ?: meta.id}.tsv` file	TSV with embeddings of BCR or TCR amino acid sequences. `*.tsv`

#2 versions_amulety tuple

`${task.process}` string	The process the versions were collected from
`amulety` string	The tool name
`amulety --help 2>&1 \| grep -o 'version [0-9\.]\+' \| grep -o '[0-9\.]\+'` eval	The command used to generate the version of the tool

#3 embedding_metadata tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*metadata.tsv` file	TSV with metadata about the embeddings. `*metadata.tsv`

Tool	Description	Homepage
amulety	Python package to create embeddings of BCR and TCR amino acid sequences.	https://amulety.readthedocs.io/en/latest/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:22:05 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Famulety%2Fembed/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/amulety/embed/blobs/sha256:db180a7f5a4f9d9cf9a1c0ea4eccb2e3ca9c200db8a917689123bd024a511669
Size	3.4 KB
Checksum	sha256:db180a7f5a4f9d9cf9a1c0ea4eccb2e3ca9c200db8a917689123bd024a511669
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:22:05 (UTC)		1	3.4 KB	-