mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
2ad98162f3
* Draft rmarkdown module * stub jupyter notebook module * Create yaml file with params * Update meta.yml for rmarkdown module * Add comment on YAML * Update notebooks module, clean up parametrize.nf * Two separate channels for parameters and input files * Fix Rmd render script * Add tests for rmarkdown * Fix tests for rmarkdown module * Update checksums * Fix tests for jupyter * Test without Grab() * Update software versions * update rmarkdown dependencies * Draft for multiple versions * Fix indent of script * Fix indent in rmarkdown script * Emit version.syml * Update modules/rmarkdown/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/rmarkdown/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/rmarkdown/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Rename rmarkdown to rmarkdownnotebook * Add rmarkdown mulled biocontainer * Write sessionInfo to separate log file * Update rmarkdownnotebook * Sessioninfo does not have a stable md5sum * Update jupyternotebook * Update meta * Add jupyternotebook biocontainers * Handle Groovy Gstrings in parameterize * Update to versions.yml * Update functions.nf * Fix versions yaml * Fix EC lint * Update modules/rmarkdownnotebook/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/jupyternotebook/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Use official test data * Harshilify * Make parameters channel clearer * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Update main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
68 lines
2 KiB
YAML
68 lines
2 KiB
YAML
name: jupyternotebook
|
|
description: |
|
|
Render jupyter (or jupytext) notebooks to HTML reports. Supports parametrization
|
|
through papermill.
|
|
keywords:
|
|
- Python
|
|
- Jupyter
|
|
- jupytext
|
|
- papermill
|
|
- notebook
|
|
- reports
|
|
tools:
|
|
- jupytext:
|
|
description: Jupyter notebooks as plain text scripts or markdown documents
|
|
homepage: https://github.com/mwouts/jupytext/
|
|
documentation: https://jupyter.org/documentation
|
|
tool_dev_url: https://github.com/mwouts/jupytext/
|
|
licence: "MIT"
|
|
- papermill:
|
|
description: Parameterize, execute, and analyze notebooks
|
|
homepage: https://github.com/nteract/papermill
|
|
documentation: http://papermill.readthedocs.io/en/latest/
|
|
tool_dev_url: https://github.com/nteract/papermill
|
|
licence: "BSD 3-clause"
|
|
- nbconvert:
|
|
description: Parameterize, execute, and analyze notebooks
|
|
homepage: https://nbconvert.readthedocs.io/en/latest/
|
|
documentation: https://nbconvert.readthedocs.io/en/latest/
|
|
tool_dev_url: https://github.com/jupyter/nbconvert
|
|
licence: "BSD 3-clause"
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- notebook:
|
|
type: file
|
|
description: Jupyter notebook or jupytext representation thereof
|
|
pattern: "*.{ipynb,py,md,Rmd,myst}"
|
|
- parameters:
|
|
type: map
|
|
description: |
|
|
Groovy map with notebook parameters which will be passed
|
|
to papermill in order to create parametrized reports.
|
|
- input_files:
|
|
type: path
|
|
description: One or multiple files serving as input data for the notebook.
|
|
pattern: "*"
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- report:
|
|
type: file
|
|
description: HTML report generated from Jupyter notebook
|
|
pattern: "*.html"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
|
|
authors:
|
|
- "@grst"
|