Description

A module to create embeddings of B-cell receptor (BCR) or T-cell receptor (TCR) 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’ (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

name:type
description
pattern

embedding

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

embedding_metadata

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

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

versions_python

${task.process}

:string

The process the versions were collected from

python

:string

The name of the tool

python --version 2>&1 | grep -o 'Python [0-9\.]\+' | grep -o '[0-9\.]\+'

:eval

The expression to obtain the version of the tool

versions_pytorch

${task.process}

:string

The process the versions were collected from

pytorch

:string

The name of the tool

python -c 'import torch; print(torch.__version__)'

:eval

The expression to obtain the version of the tool

versions_transformers

${task.process}

:string

The process the versions were collected from

transformers

:string

The name of the tool

python -c 'import transformers; print(transformers.__version__)'

:eval

The expression to obtain 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

${task.process}

:string

The process the versions were collected from

python

:string

The name of the tool

python --version 2>&1 | grep -o 'Python [0-9\.]\+' | grep -o '[0-9\.]\+'

:eval

The expression to obtain the version of the tool

${task.process}

:string

The process the versions were collected from

pytorch

:string

The name of the tool

python -c 'import torch; print(torch.__version__)'

:eval

The expression to obtain the version of the tool

${task.process}

:string

The process the versions were collected from

transformers

:string

The name of the tool

python -c 'import transformers; print(transformers.__version__)'

:eval

The expression to obtain 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
included in
airrflow
maintainer
Github user ggabernet
get in touch
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