nf-core/sambamba/depth @ 0.0.0-0c7146d
Summary
Outputs a coverage file from bam files
Get started
Add the following snippet to your workflow script to include this module.
include { SAMBAMBA_DEPTH } from 'nf-core/sambamba/depth'
License
MIT License
Process
Name
|
SAMBAMBA_DEPTH |
|---|
Input
3 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
bam
file
|
BAM file *.{bam}
|
bai
file
|
BAI file *.{bai}
|
#2
tuple
meta2
map
|
Groovy Map containing regions information |
|---|---|
bed
file
|
bed file *.{bed}
|
mode
string
|
Analysis mode can be region, window, base region|window|base
|
|---|
Output
2 channels
#1
bed
tuple
meta
map
|
Groovy Map containing sample information |
|---|---|
*.bed
file
|
bed file *.bed
|
#2
versions_sambamba
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
sambamba
string
|
The tool name |
sambamba --version 2>&1 | grep -oPm1 'sambamba \\K[0-9.]+'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| sambamba | Tools for working with SAM/BAM data | https://lomereiter.github.io/sambamba/docs/sambamba-view.html |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:33:03 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsambamba%2Fdepth/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/sambamba/depth/blobs/sha256:a89e7b4f5bdb70b4fe35be00830063b8a7f4da66e7282742d9a7ff5e5f02bc49 |
| Size | 2.6 KB |
| Checksum | sha256:a89e7b4f5bdb70b4fe35be00830063b8a7f4da66e7282742d9a7ff5e5f02bc49 |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:41:53 (UTC) | 3 | 2.6 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:33:03 (UTC) | 4 | 2.6 KB |