nf-core/samtools/depth @ 0.0.0-0c7146d
Summary
Computes the depth at each position or region.
Get started
Add the following snippet to your workflow script to include this module.
include { SAMTOOLS_DEPTH } from 'nf-core/samtools/depth'
License
MIT License
Process
Name
|
SAMTOOLS_DEPTH |
|---|
Input
2 channels
#1
tuple
meta1
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bam
file
|
sorted BAM/CRAM/SAM file *.{bam,cram,sam}
|
index
file
|
BAM/CRAM index file *.{bai,crai}
|
#2
tuple
meta2
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
intervals
file
|
list of positions or regions in specified bed file *.{bed}
|
Output
2 channels
#1
tsv
tuple
meta1
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.tsv
file
|
The output of samtools depth has three columns - the name of the contig or chromosome, the position and the number of reads aligned at that position *.{tsv}
|
#2
versions_samtools
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
samtools
string
|
The tool name |
samtools version | sed "1!d;s/.* //"
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| samtools | Tools for dealing with SAM, BAM and CRAM files; samtools depth – computes the read depth at each position or region | http://www.htslib.org |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:09:58 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fdepth/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/samtools/depth/blobs/sha256:5d25841cecb8dab8958fcb9d2616a3277ceb6cdf2fd1623c0c5dcb96828d8869 |
| Size | 2.7 KB |
| Checksum | sha256:5d25841cecb8dab8958fcb9d2616a3277ceb6cdf2fd1623c0c5dcb96828d8869 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:09:58 (UTC) | 1 | 2.7 KB | - |