nf-core/atlas/splitmerge @ 0.0.0-6c4ed3a
Summary
split single end read groups by length and merge paired end reads
Get started
Add the following snippet to your workflow script to include this module.
include { ATLAS_SPLITMERGE } from 'nf-core/atlas/splitmerge'
License
MIT License
Name
|
ATLAS_SPLITMERGE |
|---|
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
|
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
|
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
|
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 | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:03:01 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fatlas%2Fsplitmerge/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/atlas/splitmerge/blobs/sha256:99b754db553450895fe0014ef729c100d528bab2f031e9a686f64f789e68a2d4 |
| Size | 2.6 KB |
| Checksum | sha256:99b754db553450895fe0014ef729c100d528bab2f031e9a686f64f789e68a2d4 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:03:01 (UTC) | 3 | 2.6 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:02:16 (UTC) | 4 | 2.6 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:43:41 (UTC) | 4 | 2.6 KB |