nf-core/bismark/deduplicate @ 0.0.0-0c7146d
Summary
Removes alignments to the same position in the genome from the Bismark mapping output.
Get started
Add the following snippet to your workflow script to include this module.
include { BISMARK_DEDUPLICATE } from 'nf-core/bismark/deduplicate'
License
MIT License
Process
Name
|
BISMARK_DEDUPLICATE |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bam
file
|
BAM file containing read alignments *.{bam}
|
Output
3 channels
#1
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.deduplicated.bam
file
|
Deduplicated output BAM file containing read alignments *.{deduplicated.bam}
|
#2
report
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.deduplication_report.txt
file
|
Bismark deduplication reports *.{deduplication_report.txt}
|
#3
versions_bismark
tuple
${task.process}
string
|
The name of the process |
|---|---|
bismark
string
|
The name of the tool |
bismark -v 2>&1 | sed -n 's/^.*Bismark Version: v//p'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| bismark | Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion. | https://github.com/FelixKrueger/Bismark |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:27:24 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbismark%2Fdeduplicate/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bismark/deduplicate/blobs/sha256:5f823ced5aaab7d492e6aeb5abeca03c8c31199cefa49a7bd6dc7db1c38fea58 |
| Size | 2.6 KB |
| Checksum | sha256:5f823ced5aaab7d492e6aeb5abeca03c8c31199cefa49a7bd6dc7db1c38fea58 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:27:24 (UTC) | 1 | 2.6 KB | - |