Init channel-based reports#87
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Pull request overview
This PR introduces an initial, reusable Nextflow module for rendering Quarto notebooks to HTML, plus a small fixture and nf-test to validate the rendering behavior.
Changes:
- Added a new
RENDER_NOTEBOOKNextflow process to runquarto renderand emit an HTML report. - Added a minimal Quarto notebook fixture intended for use in tests.
- Added an nf-test for
RENDER_NOTEBOOKto validate process success and output production.
Reviewed changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 5 comments.
| File | Description |
|---|---|
modules/local/report/render_notebook.nf |
New module to render a provided .qmd into an HTML report via quarto render. |
tests/fixtures/test.qmd |
New Quarto fixture notebook used as the render input for the module test. |
tests/modules/local/report/render_notebook.nf.test |
New nf-test covering the RENDER_NOTEBOOK module output behavior. |
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| --- | ||
| title: "test notebook" | ||
| format: html | ||
| engine: knitr | ||
| --- | ||
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| ```{python} | ||
| print("Hello world!") | ||
| ``` |
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i'd still like to execute the test as opposed to a stub-style run.
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
This reverts commit 9e398cf.
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This pull request adds support for rendering Quarto notebooks to HTML as part of the workflow, along with a test and a sample notebook for validation. The main changes include introducing a new Nextflow process for rendering, adding a test notebook fixture, and creating a corresponding test to ensure correct functionality.
Notebook rendering feature:
RENDER_NOTEBOOKinmodules/local/report/render_notebook.nfto render Quarto.qmdnotebooks to HTML using thequarto rendercommand. The process accepts notebook and metadata inputs, and outputs an HTML file.Testing and fixtures:
test.qmdintests/fixtures/using theknitrengine for compatibility, to serve as a test input.tests/modules/local/report/render_notebook.nf.testto verify that theRENDER_NOTEBOOKprocess correctly renders a basic notebook to HTML, including assertions for process success and output.