nf-core/sambamba/markdup @ 0.0.0-3fc6d40
Summary
find and mark duplicate reads in BAM file
Get started
Add the following snippet to your workflow script to include this module.
include { SAMBAMBA_MARKDUP } from 'nf-core/sambamba/markdup'
License
MIT License
Process
Name
|
SAMBAMBA_MARKDUP |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bam
file
|
BAM/CRAM/SAM file *.{bam,cram,sam}
|
Output
3 channels
#1
bai
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.bai
file
|
An optional BAM index file. *.{bai}
|
#2
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.bam
file
|
Sorted BAM/CRAM/SAM file *.{bam,cram,sam}
|
#3
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| sambamba | process your BAM data faster! | https://lomereiter.github.io/sambamba/docs/sambamba-view.html |
| Version | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:29:27 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsambamba%2Fmarkdup/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/sambamba/markdup/blobs/sha256:0ba79748107427b0d43609ab7c58487f66decc7b31b7d33ed848e41fc1fce794 |
| Size | 2.1 KB |
| Checksum | sha256:0ba79748107427b0d43609ab7c58487f66decc7b31b7d33ed848e41fc1fce794 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:41:55 (UTC) | 3 | 2.1 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:29:27 (UTC) | 3 | 2.1 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:33:06 (UTC) | 4 | 2.1 KB |