nf-core/samtools/markdup @ 0.0.0-6c4ed3a
Summary
mark duplicate alignments in a coordinate sorted file
Get started
Add the following snippet to your workflow script to include this module.
include { SAMTOOLS_MARKDUP } from 'nf-core/samtools/markdup'
License
MIT License
Process
Name
|
SAMTOOLS_MARKDUP |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
input
file
|
BAM/CRAM/SAM file *.{bam,cram,sam}
|
#2
tuple
meta2
map
|
Groovy Map containing reference information e.g. [ id:'genome' ] |
|---|---|
fasta
file
|
Reference genome file *.{fa,fasta}
|
fai
file
|
Reference genome index file *.fai
|
Output
4 channels
#1
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.bam
file
|
BAM file *{.bam}
|
#2
sam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.sam
file
|
SAM file *{.sam}
|
#3
cram
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.cram
file
|
CRAM file *{.cram}
|
#4
versions_samtools
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
samtools
string
|
The tool name |
samtools version | sed '1!d;s/.* //'
string
|
The command used to generate the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| samtools | Tools for dealing with SAM, BAM and CRAM files | http://www.htslib.org |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:43:17 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fmarkdup/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/samtools/markdup/blobs/sha256:3f5457bee823873a0d385b4fb1d636c50352179e28f29e1e65e0e09568b38bbe |
| Size | 2.8 KB |
| Checksum | sha256:3f5457bee823873a0d385b4fb1d636c50352179e28f29e1e65e0e09568b38bbe |
| Downloads | 5 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:43:17 (UTC) | 5 | 2.8 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:33:58 (UTC) | 2 | 2.8 KB |