Nextflow Registry | nf-core/atlas/splitmerge@0.0.0-0c7146d

nf-core/atlas/splitmerge @ 0.0.0-0c7146d

split single end read groups by length and merge paired end reads

split merge bam read group

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @merszym

Maintainers: @merszym

split single end read groups by length and merge paired end reads

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

include { ATLAS_SPLITMERGE } from 'nf-core/atlas/splitmerge'

MIT License

Process

`Name`	`ATLAS_SPLITMERGE`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	Single input BAM file. `*.bam`
`bai` file	The BAI file for the input BAM file `*.bai`
`read_group_settings` file	TXT file containing the split and merge settings for each readgroup. Each line consist of one readgroup, single/double identifier and the maximum cycle number of the sequencer. e.g. "RG1 single 100" `*.txt`
`blacklist` file	blacklist.txt (optional), A txt file with blacklisted read names that should be ignored and just written to file, each on a new line `*.txt`

Output 3 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_mergedReads.bam` file	A BAM file with suffix_mergedReads.bam `*_mergedReads.bam`

#2 txt tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.txt.gz` file	A file listing all reads that were filtered out in the merging process with suffix_ignoredReads.txt.gz `*.txt.gz`

#3 versions_atlas tuple

`${task.process}` string	The name of the process
`atlas` string	The name of the tool
`atlas \| sed -e '2!d;s/.*Atlas //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
atlas	ATLAS, a suite of methods to accurately genotype and estimate genetic diversity	https://bitbucket.org/wegmannlab/atlas/wiki/Home

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:23:10 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fatlas%2Fsplitmerge/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/atlas/splitmerge/blobs/sha256:2f44e6ad55fa00d38e1b21bb2dee86729f78a2c4a26d2e1359038ab424ed9421
Size	2.6 KB
Checksum	sha256:2f44e6ad55fa00d38e1b21bb2dee86729f78a2c4a26d2e1359038ab424ed9421
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:23:10 (UTC)		1	2.6 KB	-