Description

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

Input

name:type
description
pattern

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’ (heavy) or ‘HL’ (heavy + light, for single-cell data).

Output

name:type
description
pattern

embedding

meta

:map

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

*.tsv

:file

TSV with BALM paired embeddings.

*.tsv

versions_amulety

${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

Topics

name:type
description
pattern

versions

${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

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
maintainer
Github user ggabernet
get in touch
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