modules/jupyternotebook

Render jupyter (or jupytext) notebooks to HTML reports. Supports parametrization through papermill.

PythonJupyterjupytextpapermillnotebookreports

https://github.com/nf-core/modules/[...]/modules/nf-core/jupyternotebook

Description

Render jupyter (or jupytext) notebooks to HTML reports. Supports parametrization through papermill.

Input

name:type

description

pattern

`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.

Output

name:type

description

pattern

`report`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.html`
`:file`

HTML report generated from Jupyter notebook

*.html

`artifacts`

`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/

`versions_jupytext`

`${task.process}`
`:string`

The name of the process

`jupytext`
`:string`

The name of the tool

`jupytext --version`
`:eval`

The expression to obtain the version of the tool

`versions_ipykernel`

`${task.process}`
`:string`

The name of the process

`ipykernel`
`:string`

The name of the tool

`python -c "import ipykernel; print(ipykernel.version)"`
`:eval`

The expression to obtain the version of the tool

`versions_nbconvert`

`${task.process}`
`:string`

The name of the process

`nbconvert`
`:string`

The name of the tool

`jupyter nbconvert --version`
`:eval`

The expression to obtain the version of the tool

`versions_papermill`

`${task.process}`
`:string`

The name of the process

`papermill`
`:string`

The name of the tool

`papermill --version | cut -f1 -d" "`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`jupytext`
`:string`

The name of the tool

`jupytext --version`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`ipykernel`
`:string`

The name of the tool

`python -c "import ipykernel; print(ipykernel.version)"`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`nbconvert`
`:string`

The name of the tool

`jupyter nbconvert --version`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`papermill`
`:string`

The name of the tool

`papermill --version | cut -f1 -d" "`
`:eval`

The expression to obtain the version of the tool

Tools

jupytext

Jupyter notebooks as plain text scripts or markdown documents

github.com/mwouts/jupytext jupyter.org/documentation https://github.com/mwouts/jupytext/

papermill

Parameterize, execute, and analyze notebooks

github.com/nteract/papermill http://papermill.readthedocs.io/en/latest https://github.com/nteract/papermill

nbconvert

Parameterize, execute, and analyze notebooks

nbconvert.readthedocs.io/en/latest https://github.com/jupyter/nbconvert

modules/jupyternotebook

Description

Input

meta:map

notebook:file

parameters:map

input_files:file

kernel_:string

Output

report

meta:map

*.html:file

artifacts

meta:map

artifacts/:directory

versions_jupytext

${task.process}:string

jupytext:string

jupytext --version:eval

versions_ipykernel

${task.process}:string

ipykernel:string

python -c "import ipykernel; print(ipykernel.__version__)":eval

versions_nbconvert

${task.process}:string

nbconvert:string

jupyter nbconvert --version:eval

versions_papermill

${task.process}:string

papermill:string

papermill --version | cut -f1 -d" ":eval

Topics

versions

${task.process}:string

jupytext:string

jupytext --version:eval

${task.process}:string

ipykernel:string

python -c "import ipykernel; print(ipykernel.__version__)":eval

${task.process}:string

nbconvert:string

jupyter nbconvert --version:eval

${task.process}:string

papermill:string

papermill --version | cut -f1 -d" ":eval

Tools

jupytext

papermill

nbconvert

maintainer

get in touch

`meta`
`:map`

`notebook`
`:file`

`parameters`
`:map`

`input_files`
`:file`

`kernel_`
`:string`

`report`

`meta`
`:map`

`*.html`
`:file`

`artifacts`

`meta`
`:map`

`artifacts/`
`:directory`

`versions_jupytext`

`${task.process}`
`:string`

`jupytext`
`:string`

`jupytext --version`
`:eval`

`versions_ipykernel`

`${task.process}`
`:string`

`ipykernel`
`:string`

`python -c "import ipykernel; print(ipykernel.version)"`
`:eval`

`versions_nbconvert`

`${task.process}`
`:string`

`nbconvert`
`:string`

`jupyter nbconvert --version`
`:eval`

`versions_papermill`

`${task.process}`
`:string`

`papermill`
`:string`

`papermill --version | cut -f1 -d" "`
`:eval`

`versions`

`${task.process}`
`:string`

`jupytext`
`:string`

`jupytext --version`
`:eval`

`${task.process}`
`:string`

`ipykernel`
`:string`

`python -c "import ipykernel; print(ipykernel.version)"`
`:eval`

`${task.process}`
`:string`

`nbconvert`
`:string`

`jupyter nbconvert --version`
`:eval`

`${task.process}`
`:string`

`papermill`
`:string`

`papermill --version | cut -f1 -d" "`
`:eval`