modules/angsd_contamination

A tool to estimate nuclear contamination in males based on heterozygosity in the female chromosome.

angsdpopulation geneticsnuclear contamination estimate

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

Description

A tool to estimate nuclear contamination in males based on heterozygosity in the female chromosome.

Input

name:type

description

pattern

`meta`
`:map`

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

`icounts`
`:file`

Internal format for dumping binary single chrs. Useful for ANGSD contamination

*.icnts.gz

`meta2`
`:map`

Groovy Map containing information related to the hapmap_file. e.g. [ id:‘test’ ]

`hapmap_file`
`:file`

A list of variable sites to look for heterozygosity.

Output

name:type

description

pattern

`txt`

`meta`
`:map`

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

`*.txt`
`:file`

Contamination estimation output.

*.txt

`versions_angsd`

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

The name of the process

`angsd`
`:string`

The name of the tool

`angsd 2>&1 | sed '1!d;s/.version: //;s/ .//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`angsd`
`:string`

The name of the tool

`angsd 2>&1 | sed '1!d;s/.version: //;s/ .//'`
`:eval`

The expression to obtain the version of the tool

Tools

angsd
GPL v3 MIT

ANGSD: Analysis of next generation Sequencing Data

http://www.popgen.dk/angsd https://github.com/ANGSD/angsd 10.1186/s12859-014-0356-4

modules/angsd_contamination

Description

Input

`meta`
`:map`

`icounts`
`:file`

`meta2`
`:map`

`hapmap_file`
`:file`

Output

`txt`

`meta`
`:map`

`*.txt`
`:file`

`versions_angsd`

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

`angsd`
`:string`

`angsd 2>&1 | sed '1!d;s/.version: //;s/ .//'`
`:eval`

Topics

`versions`

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

`angsd`
`:string`

`angsd 2>&1 | sed '1!d;s/.version: //;s/ .//'`
`:eval`

Tools

angsd
GPL v3 MIT

maintainer

get in touch

modules/angsd_contamination

Description

Input

meta:map

icounts:file

meta2:map

hapmap_file:file

Output

txt

meta:map

*.txt:file

versions_angsd

${task.process}:string

angsd:string

angsd 2>&1 | sed '1!d;s/.*version: //;s/ .*//':eval

Topics

versions

${task.process}:string

angsd:string

angsd 2>&1 | sed '1!d;s/.*version: //;s/ .*//':eval

Tools

angsd GPL v3 MIT

maintainer

get in touch

`meta`
`:map`

`icounts`
`:file`

`meta2`
`:map`

`hapmap_file`
`:file`

`txt`

`meta`
`:map`

`*.txt`
`:file`

`versions_angsd`

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

`angsd`
`:string`

`angsd 2>&1 | sed '1!d;s/.version: //;s/ .//'`
`:eval`

`versions`

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

`angsd`
`:string`

`angsd 2>&1 | sed '1!d;s/.version: //;s/ .//'`
`:eval`

angsd
GPL v3 MIT