nf-core/biobambam/bammarkduplicates2 @ 0.0.0-0c7146d
Summary
Locate and tag duplicate reads in a BAM file
Get started
Add the following snippet to your workflow script to include this module.
include { BIOBAMBAM_BAMMARKDUPLICATES2 } from 'nf-core/biobambam/bammarkduplicates2'
License
MIT License
Process
Name
|
BIOBAMBAM_BAMMARKDUPLICATES2 |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bam
file
|
BAM/CRAM file *.{bam,cram}
|
Output
3 channels
#1
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.bam
file
|
BAM file with duplicate reads marked/removed *.{bam}
|
#2
metrics
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.metrics.txt
file
|
Duplicate metrics file generated by biobambam *.{metrics.txt}
|
#3
versions_biobambam
tuple
${task.process}
string
|
The name of the process |
|---|---|
biobambam
string
|
The name of the tool |
bammarkduplicates2 --version |& sed '1!d; s/.*version //; s/.\$//'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| biobambam | biobambam is a set of tools for early stage alignment file processing. | https://gitlab.com/german.tischler/biobambam2 |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 18:47:35 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fbiobambam%2Fbammarkduplicates2/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/biobambam/bammarkduplicates2/blobs/sha256:65dde58ca768ae189a3d1577a9bfffff1fd08405e85be8cd1f7985a563a63104 |
| Size | 2.5 KB |
| Checksum | sha256:65dde58ca768ae189a3d1577a9bfffff1fd08405e85be8cd1f7985a563a63104 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:06:05 (UTC) | 3 | 2.6 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:04:08 (UTC) | 3 | 2.6 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:47:35 (UTC) | 3 | 2.5 KB |