modules/haplocheck

Haplocheck detects contamination patterns in mtDNA AND WGS sequencing studies by analyzing the mitochondrial DNA. Haplocheck also works as a proxy tool for nDNA studies and provides users a graphical report to investigate the contamination further. Internally, it uses the Haplogrep tool, that supports rCRS and RSRS mitochondrial versions.

mitochondrialmtDNAcontamination

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

Description

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`vcf`
`:file`

VCF file

*.{vcf.gz}

Output

name:type

description

pattern

`txt`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.txt`
`:file`

Raw report in txt format

*.{txt}

`html`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.html`
`:file`

Haplocheck HTML report

*.{html}

`versions_haplocheck`

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

The name of the process

`haplocheck`
`:string`

The name of the tool

`haplocheck --version 2>&1 | sed -n 's/^haplocheck //p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`haplocheck`
`:string`

The name of the tool

`haplocheck --version 2>&1 | sed -n 's/^haplocheck //p'`
`:eval`

The expression to obtain the version of the tool

Tools

haplocheck
MIT

Detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitochondrial content.

github.com/genepi/haplocheck 10.1101/gr.256545.119

modules/haplocheck

Description

Input

`meta`
`:map`

`vcf`
`:file`

Output

`txt`

`meta`
`:map`

`*.txt`
`:file`

`html`

`meta`
`:map`

`*.html`
`:file`

`versions_haplocheck`

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

`haplocheck`
`:string`

`haplocheck --version 2>&1 | sed -n 's/^haplocheck //p'`
`:eval`

Topics

`versions`

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

`haplocheck`
`:string`

`haplocheck --version 2>&1 | sed -n 's/^haplocheck //p'`
`:eval`

Tools

haplocheck
MIT

included in

maintainer

get in touch

modules/haplocheck

Description

Input

meta:map

vcf:file

Output

txt

meta:map

*.txt:file

html

meta:map

*.html:file

versions_haplocheck

${task.process}:string

haplocheck:string

haplocheck --version 2>&1 | sed -n 's/^haplocheck //p':eval

Topics

versions

${task.process}:string

haplocheck:string

haplocheck --version 2>&1 | sed -n 's/^haplocheck //p':eval

Tools

haplocheck MIT

included in

maintainer

get in touch

`meta`
`:map`

`vcf`
`:file`

`txt`

`meta`
`:map`

`*.txt`
`:file`

`html`

`meta`
`:map`

`*.html`
`:file`

`versions_haplocheck`

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

`haplocheck`
`:string`

`haplocheck --version 2>&1 | sed -n 's/^haplocheck //p'`
`:eval`

`versions`

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

`haplocheck`
`:string`

`haplocheck --version 2>&1 | sed -n 's/^haplocheck //p'`
`:eval`

haplocheck
MIT