Nextflow Registry | nf-core/tmb/pytmb@0.0.0-0c7146d

nf-core/tmb/pytmb @ 0.0.0-0c7146d

This module calculates Tumor Mutational Burden (TMB) scores from VCF files using the pyTMB tool.

tumor mutation burden score

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @georgiakes

Maintainers: @georgiakes

This module calculates Tumor Mutational Burden (TMB) scores from VCF files using the pyTMB tool.

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

include { TMB_PYTMB } from 'nf-core/tmb/pytmb'

MIT License

Process

`Name`	`TMB_PYTMB`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`vcf` file	Annotated VCF file. `*.vcf`
`bed` file	BED file defining the target regions. Required if `eff_genome_size` is not provided. `*.bed`
`eff_genome_size` string	Effective genome size (in bases). Required if `bed` is not provided.
`var_config` file	YAML file defining variant annotation parsing rules. See example here. `*.yml`
`db_config` file	YAML file defining the database configuration for variant annotations. See example here. `*.yml`

Output 4 channels

#1 tmb_log tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.log` file	Log file containing TMB calculation details

#2 debug_vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_debug.vcf.gz` file	Debug VCF file containing detailed TMB calculation information `*_debug.vcf.gz`

#3 export_vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_export.vcf.gz` file	Export VCF file containing TMB annotations `*_export.vcf.gz`

#4 versions_tmb tuple

`${task.process}` string	The name of the process
`tmb` string	The name of the tool
`pyTMB.py --version \| awk '{print \$2}' \| tr -d '()'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
tmb	This tool was designed to calculate a Tumor Mutational Burden (TMB) score from a VCF file.	https://github.com/bioinfo-pf-curie/TMB/blob/v1.5.0/README.md

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:19:40 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Ftmb%2Fpytmb/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/tmb/pytmb/blobs/sha256:6b8a7214fca282eee7e6cb7beb66c19519f927b8d4cc0069fc1b663b52c6a9a8
Size	3.4 KB
Checksum	sha256:6b8a7214fca282eee7e6cb7beb66c19519f927b8d4cc0069fc1b663b52c6a9a8
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:19:40 (UTC)		1	3.4 KB	-