nf-core/haplocheck @ 0.0.0-0c7146d
Summary
Haplocheck detects contamination patterns in mtDNA AND WGS sequencing studies by analyzing the mitochondrial DNA. Haplocheck also works as a proxy tool for nDNA studies and provides users a graphical report to investigate the contamination further. Internally, it uses the Haplogrep tool, that supports rCRS and RSRS mitochondrial versions.
Get started
Add the following snippet to your workflow script to include this module.
include { HAPLOCHECK } from 'nf-core/haplocheck'
License
MIT License
Process
Name
|
HAPLOCHECK |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
vcf
file
|
VCF file *.{vcf.gz}
|
Output
3 channels
#1
txt
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.txt
file
|
Raw report in txt format *.{txt}
|
#2
html
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.html
file
|
Haplocheck HTML report *.{html}
|
#3
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| haplocheck | Detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitochondrial content. | https://github.com/genepi/haplocheck |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:46:47 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fhaplocheck/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/haplocheck/blobs/sha256:97b387df9b525efa679cc17a4b21416a641ee1e6e8b5a792a2f8f4c2e1d6ca9c |
| Size | 2.4 KB |
| Checksum | sha256:97b387df9b525efa679cc17a4b21416a641ee1e6e8b5a792a2f8f4c2e1d6ca9c |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:46:47 (UTC) | 1 | 2.4 KB | - |