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 | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:26:50 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbiobambam%2Fbammarkduplicates2/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/biobambam/bammarkduplicates2/blobs/sha256:88044d9b72ab45ffb2432d143f251dfbb77a0079f6f2b76b75d3195e2cee89cd |
| Size | 2.6 KB |
| Checksum | sha256:88044d9b72ab45ffb2432d143f251dfbb77a0079f6f2b76b75d3195e2cee89cd |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:26:50 (UTC) | 1 | 2.6 KB | - |