nf-core/modkit/repair @ 0.0.0-0c7146d
Summary
Repair the MM/ML tags on trimmed or hard-clipped ONT reads using untrimmed ONT reads.
Get started
Add the following snippet to your workflow script to include this module.
include { MODKIT_REPAIR } from 'nf-core/modkit/repair'
License
MIT License
Process
Name
|
MODKIT_REPAIR |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
before_trim
file
|
Sorted BAM file *.{bam}
|
after_trim
file
|
Sorted BAM file *.{bam}
|
Output
3 channels
#1
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.bam
file
|
Sorted BAM file *.{bam}
|
#2
log
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.log
file
|
File for debug logs to be written to *.log
|
#3
versions_modkit
tuple
${task.process}
string
|
The name of the process |
|---|---|
modkit
string
|
The name of the tool |
modkit --version | sed 's/modkit //'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| modkit | A bioinformatics tool for working with modified bases in Oxford Nanopore sequencing data. | https://nanoporetech.github.io/modkit/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:19:51 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fmodkit%2Frepair/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/modkit/repair/blobs/sha256:913ab9c0cf19c3ace339b9c418ab4c424e624470e07b7abfc08230335edd4893 |
| Size | 2.5 KB |
| Checksum | sha256:913ab9c0cf19c3ace339b9c418ab4c424e624470e07b7abfc08230335edd4893 |
| Downloads | 2 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:32:09 (UTC) | 4 | 2.5 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:22:54 (UTC) | 3 | 2.6 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:19:51 (UTC) | 2 | 2.5 KB |