nf-core/jupyternotebook @ 0.0.0-0c7146d
Summary
Render jupyter (or jupytext) notebooks to HTML reports. Supports parametrization through papermill.
Get started
Add the following snippet to your workflow script to include this module.
include { JUPYTERNOTEBOOK } from 'nf-core/jupyternotebook'
License
MIT License
Name
|
JUPYTERNOTEBOOK |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
notebook
file
|
Jupyter notebook or jupytext representation thereof *.{ipynb,py,md,Rmd,myst}
|
parameters
map
|
Groovy map with notebook parameters which will be passed to papermill in order to create parametrized reports. |
|---|
input_files
file
|
One or multiple files serving as input data for the notebook. *
|
|---|
kernel_
string
|
Name of the kernel to use. |
|---|
report
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.html
file
|
HTML report generated from Jupyter notebook *.html
|
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
artifacts
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
artifacts/
directory
|
Directory containing all artifacts generated by the notebook artifacts/
|
| Tool | Description | Homepage |
|---|---|---|
| jupytext | Jupyter notebooks as plain text scripts or markdown documents | https://github.com/mwouts/jupytext/ |
| papermill | Parameterize, execute, and analyze notebooks | https://github.com/nteract/papermill |
| nbconvert | Parameterize, execute, and analyze notebooks | https://nbconvert.readthedocs.io/en/latest/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:12:11 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fjupyternotebook/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/jupyternotebook/blobs/sha256:443b0f7b7626d53da093dfceb305b2810646295ed0211419c4d873c6a3399cba |
| Size | 3.6 KB |
| Checksum | sha256:443b0f7b7626d53da093dfceb305b2810646295ed0211419c4d873c6a3399cba |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:26:22 (UTC) | 4 | 3.6 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:18:21 (UTC) | 2 | 3.6 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:12:11 (UTC) | 3 | 3.6 KB |