Nextflow Registry | nf-core/angsd/docounts@0.0.0-0c7146d

nf-core/angsd/docounts @ 0.0.0-0c7146d

Calculates base frequency statistics across reference positions from BAM.

angsd population genetics allele counts doCounts

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @jfy133

Maintainers: @jfy133

Calculates base frequency statistics across reference positions from BAM.

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

include { ANGSD_DOCOUNTS } from 'nf-core/angsd/docounts'

MIT License

Process

`Name`	`ANGSD_DOCOUNTS`

Input 1 channel

#1 tuple

`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 7 channels

#1 qs tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.qs` file	Distribution of scores `*.qs`

#2 pos tuple

`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`

#3 counts tuple

`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`

#4 icounts tuple

`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`

#5 depth_global tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.depthGlobal` file	Distribution of sequencing depths `*.depthGlobal`

#6 depth_sample tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.depthSample` file	Distribution of sequencing depths `*.depthSample`

#7 versions_angsd tuple

`${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

Tool	Description	Homepage
angsd	ANGSD: Analysis of next generation Sequencing Data	http://www.popgen.dk/angsd/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:22:14 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fangsd%2Fdocounts/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/angsd/docounts/blobs/sha256:0eac2abde8ce7092108815eff0eb07c09fcbce2e855c3cd0291c8ac45a35c09b
Size	3.4 KB
Checksum	sha256:0eac2abde8ce7092108815eff0eb07c09fcbce2e855c3cd0291c8ac45a35c09b