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* 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
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description: |
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Render jupyter (or jupytext) notebooks to HTML reports. Supports parametrization
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through papermill.
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keywords:
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- Python
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- Jupyter
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- jupytext
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- papermill
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- notebook
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- reports
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tools:
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- jupytext:
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description: Jupyter notebooks as plain text scripts or markdown documents
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homepage: https://github.com/mwouts/jupytext/
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documentation: https://jupyter.org/documentation
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tool_dev_url: https://github.com/mwouts/jupytext/
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licence: "MIT"
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- papermill:
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description: Parameterize, execute, and analyze notebooks
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homepage: https://github.com/nteract/papermill
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documentation: http://papermill.readthedocs.io/en/latest/
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tool_dev_url: https://github.com/nteract/papermill
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licence: "BSD 3-clause"
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- nbconvert:
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description: Parameterize, execute, and analyze notebooks
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homepage: https://nbconvert.readthedocs.io/en/latest/
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documentation: https://nbconvert.readthedocs.io/en/latest/
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tool_dev_url: https://github.com/jupyter/nbconvert
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licence: "BSD 3-clause"
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- notebook:
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type: file
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description: Jupyter notebook or jupytext representation thereof
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pattern: "*.{ipynb,py,md,Rmd,myst}"
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- parameters:
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type: map
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description: |
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Groovy map with notebook parameters which will be passed
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to papermill in order to create parametrized reports.
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- input_files:
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type: path
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description: One or multiple files serving as input data for the notebook.
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pattern: "*"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- report:
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type: file
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description: HTML report generated from Jupyter notebook
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pattern: "*.html"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@grst"
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