Description

A module to translate BCR and TCR nucleotide sequences into amino acid sequences using amulety and igblast.

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}

reference_igblast

:file

Built reference databases for igblast

Output

name:type
description
pattern

repertoire_translated

meta

:map

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

*_translated.tsv

:file

TSV with BCR/TCR amino acid sequences in AIRR rearrangement format

*.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_igblastn

${task.process}

:string

The process the versions were collected from

igblastn

:string

The tool name

igblastn -version | grep -o 'igblast[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

igblastn

:string

The tool name

igblastn -version | grep -o 'igblast[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

igblast
United States Government Work

A tool for immunoglobulin (IG, BCR) and T cell receptor (TCR) V domain sequences blasting.

ncbi.nlm.nih.gov/igblast ncbi.github.io/igblast https://github.com/ncbi/igblast 10.1093/nar/gkt382
included in
airrflow
maintainer
Github user ggabernet
get in touch
Ask a question on Slack Open an issue on GitHub