Description

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

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}

reference_igblast{:bash}

:file

Built reference databases for igblast

Output

name:type
description
pattern

repertoire_translated{:bash}

meta{:bash}

:map

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

*_translated.tsv{:bash}

:file

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

*.tsv

versions_amulety{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

amulety{:bash}

:string

The tool name

amulety --help 2>&1 | grep -o 'version [0-9\.]\+' | grep -o '[0-9\.]\+'{:bash}

:string

The command used to generate the version of the tool

versions_igblastn{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

igblastn{:bash}

:string

The tool name

igblastn -version | grep -o 'igblast[0-9\. ]\+' | grep -o '[0-9\. ]\+'{:bash}

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

amulety{:bash}

:string

The tool name

amulety --help 2>&1 | grep -o 'version [0-9\.]\+' | grep -o '[0-9\.]\+'{:bash}

:string

The command used to generate the version of the tool

${task.process}{:bash}

:string

The process the versions were collected from

igblastn{:bash}

:string

The tool name

igblastn -version | grep -o 'igblast[0-9\. ]\+' | grep -o '[0-9\. ]\+'{:bash}

:string

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

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