modules/tmb_pytmb

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

tumormutationburdenscore

https://github.com/nf-core/modules/[...]/modules/nf-core/tmb/pytmb

Description

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

Input

name:type

description

pattern

`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

name:type

description

pattern

`tmb_log`

`meta`
`:map`

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

`*.log`
`:file`

Log file containing TMB calculation details

`export_vcf`

`meta`
`:map`

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

`*_export.vcf.gz`
`:file`

Export VCF file containing TMB annotations

*_export.vcf.gz

`debug_vcf`

`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

`versions_tmb`

`${task.process}`
`:string`

The name of the process

`tmb`
`:string`

The name of the tool

`pyTMB --version | awk '{print \$2}' | tr -d '()'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`tmb`
`:string`

The name of the tool

`pyTMB --version | awk '{print \$2}' | tr -d '()'`
`:eval`

The expression to obtain the version of the tool

Tools

tmb
CeCILL FREE SOFTWARE LICENSE AGREEMENT

This tool was designed to calculate a Tumor Mutational Burden (TMB) score from a VCF file.

github.com/bioinfo-pf-curie/TMB/blob/v1.5.0/README.md https://github.com/bioinfo-pf-curie/TMB 10.1186/s12915-024-01839-8

modules/tmb_pytmb

Description

Input

`meta`
`:map`

`vcf`
`:file`

`bed`
`:file`

`eff_genome_size`
`:string`

`var_config`
`:file`

`db_config`
`:file`

Output

`tmb_log`

`meta`
`:map`

`*.log`
`:file`

`export_vcf`

`meta`
`:map`

`*_export.vcf.gz`
`:file`

`debug_vcf`

`meta`
`:map`

`*_debug.vcf.gz`
`:file`

`versions_tmb`

`${task.process}`
`:string`

`tmb`
`:string`

`pyTMB --version | awk '{print \$2}' | tr -d '()'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`tmb`
`:string`

`pyTMB --version | awk '{print \$2}' | tr -d '()'`
`:eval`

Tools

tmb
CeCILL FREE SOFTWARE LICENSE AGREEMENT

maintainer

get in touch

modules/tmb_pytmb

Description

Input

meta :map

vcf :file

bed :file

eff_genome_size :string

var_config :file

db_config :file

Output

tmb_log

meta :map

*.log :file

export_vcf

meta :map

*_export.vcf.gz :file

debug_vcf

meta :map

*_debug.vcf.gz :file

versions_tmb

${task.process} :string

tmb :string

pyTMB --version | awk '{print \$2}' | tr -d '()' :eval

Topics

versions

${task.process} :string

tmb :string

pyTMB --version | awk '{print \$2}' | tr -d '()' :eval

Tools

tmbCeCILL FREE SOFTWARE LICENSE AGREEMENT

maintainer

get in touch

`meta`
`:map`

`vcf`
`:file`

`bed`
`:file`

`eff_genome_size`
`:string`

`var_config`
`:file`

`db_config`
`:file`

`tmb_log`

`meta`
`:map`

`*.log`
`:file`

`export_vcf`

`meta`
`:map`

`*_export.vcf.gz`
`:file`

`debug_vcf`

`meta`
`:map`

`*_debug.vcf.gz`
`:file`

`versions_tmb`

`${task.process}`
`:string`

`tmb`
`:string`

`pyTMB --version | awk '{print \$2}' | tr -d '()'`
`:eval`

`versions`

`${task.process}`
`:string`

`tmb`
`:string`

`pyTMB --version | awk '{print \$2}' | tr -d '()'`
`:eval`

tmb
CeCILL FREE SOFTWARE LICENSE AGREEMENT