modules/angsd_docounts

Calculates base frequency statistics across reference positions from BAM.

angsdpopulation geneticsallele countsdoCounts

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

Description

Calculates base frequency statistics across reference positions from BAM.

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

A list of BAM or CRAM files

*.{bam,cram}

`bai`
`:file`

List of BAM/CRAM index files

*.{bai,csi}

`minqfile`
`:file`

File with individual quality score thresholds

*

Output

name:type

description

pattern

`depth_sample`

`meta`
`:map`

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

`*.depthSample`
`:file`

Distribution of sequencing depths

*.depthSample

`depth_global`

`meta`
`:map`

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

`*.depthGlobal`
`:file`

Distribution of sequencing depths

*.depthGlobal

`qs`

`meta`
`:map`

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

`*.qs`
`:file`

Distribution of scores

*.qs

`pos`

`meta`
`:map`

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

`*.pos.gz`
`:file`

Various types of depth statistics (depending on value for -dumpCounts)

*.pos.gz

`counts`

`meta`
`:map`

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

`*.counts.gz`
`:file`

Various types of statistics (related to pos.gz)

*.counts.gz

`icounts`

`meta`
`:map`

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

`*.icnts.gz`
`:file`

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

*.icnts.gz

`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_docounts

Description

Input

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`minqfile`
`:file`

Output

`depth_sample`

`meta`
`:map`

`*.depthSample`
`:file`

`depth_global`

`meta`
`:map`

`*.depthGlobal`
`:file`

`qs`

`meta`
`:map`

`*.qs`
`:file`

`pos`

`meta`
`:map`

`*.pos.gz`
`:file`

`counts`

`meta`
`:map`

`*.counts.gz`
`:file`

`icounts`

`meta`
`:map`

`*.icnts.gz`
`: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_docounts

Description

Input

meta:map

bam:file

bai:file

minqfile:file

Output

depth_sample

meta:map

*.depthSample:file

depth_global

meta:map

*.depthGlobal:file

qs

meta:map

*.qs:file

pos

meta:map

*.pos.gz:file

counts

meta:map

*.counts.gz:file

icounts

meta:map

*.icnts.gz: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`

`bam`
`:file`

`bai`
`:file`

`minqfile`
`:file`

`depth_sample`

`meta`
`:map`

`*.depthSample`
`:file`

`depth_global`

`meta`
`:map`

`*.depthGlobal`
`:file`

`qs`

`meta`
`:map`

`*.qs`
`:file`

`pos`

`meta`
`:map`

`*.pos.gz`
`:file`

`counts`

`meta`
`:map`

`*.counts.gz`
`:file`

`icounts`

`meta`
`:map`

`*.icnts.gz`
`: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