nf-core/bamutil/clipoverlap @ 0.0.0-3fc6d40
Summary
clips overlapping read pairs. When two mates overlap, this tool will clip the record's whose clipped region would have the lowest average quality.
Get started
Add the following snippet to your workflow script to include this module.
include { BAMUTIL_CLIPOVERLAP } from 'nf-core/bamutil/clipoverlap'
License
MIT License
Process
Name
|
BAMUTIL_CLIPOVERLAP |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
bam
file
|
Coordinate/ReadName sorted BAM/SAM/uncompressedBAM file *.{bam,sam,ubam}
|
Output
3 channels
#1
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.bam
file
|
Coordinate/ReadName sorted BAM/SAM/uncompressedBAM file *.{bam}
|
#2
stats_log
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.log
file
|
basic overlap statistics when unabled with --stats *.{log}
|
#3
versions_bamutil
tuple
${task.process}
string
|
The name of the process |
|---|---|
bamutil
string
|
The name of the tool |
bam clipOverlap 2>&1 | grep '^Version:' | sed 's/^Version: //;s/;.*//'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| bamutil | Programs that perform operations on SAM/BAM files, all built into a single executable, bam. | https://genome.sph.umich.edu/wiki/BamUtil |
| Version | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:03:20 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fbamutil%2Fclipoverlap/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bamutil/clipoverlap/blobs/sha256:307722428726954a3dbfa59c72c4e55520168219f56eb6db0f2cf5660c9476e3 |
| Size | 2.5 KB |
| Checksum | sha256:307722428726954a3dbfa59c72c4e55520168219f56eb6db0f2cf5660c9476e3 |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:04:28 (UTC) | 3 | 2.5 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:03:20 (UTC) | 4 | 2.5 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:45:08 (UTC) | 3 | 2.5 KB |