Update to match the current nf-core/modules repo#5
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Pull Request Overview
This PR updates the nf-core/modules-template to match the current nf-core/modules repository structure. The update introduces improved nf-test support with test run sharding, updates GitHub Actions workflows for better CI/CD, and addresses template variables and instructions as mentioned in issue #2.
- Introduced comprehensive nf-test configuration with sharding support for parallel test execution
- Updated GitHub Actions workflows to separate linting and testing responsibilities
- Added new schema validation files for modules and subworkflows
Reviewed Changes
Copilot reviewed 33 out of 33 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| tests/demo-answers.yml | Updated copyright field name from year to date |
| nf-modules-template/tests/config/nextflow.config | Increased memory allocation for test processes |
| nf-modules-template/nf-test.config | Updated plugin versions and added nft-utils plugin |
| nf-modules-template/.github/workflows/ | Replaced single test workflow with separate lint and nf-test workflows |
| nf-modules-template/.github/actions/ | Added reusable GitHub Actions for test sharding and execution |
| nf-modules-template/modules/meta-schema.json | Enhanced schema validation for module metadata |
| nf-modules-template/README.md.jinja | Added comprehensive documentation for sub-workflows and cross-organization modules |
| copier.yml | Fixed template variable naming and updated defaults |
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mashehu
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mashehu
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Didn't go through everything yet, but need to stop for now.
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how does this filename work? Shouldn't the if clause be starting at .github/?
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That's how it was set up before me 🤷🏼♂️
I can just say that it's creating .github/workflows/lint.yml just fine.
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I understand this a bit better. The Jinja variable controls the CI only ("What CI provider will you use for testing?"). There are other files in .github/ like CONTRIBUTING.md that are useful even if the CI isn't turned on.
But for these, I made a conditional directory using the repo_host variable
…t allowance of runners
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I pushed a bunch of commits to match the latest nf-core/modules |
| tests/data/ | ||
| work/ | ||
| .github/CODEOWNERS-tmp | ||
| modules/nf-core |
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is this to avoid checking in nf-core modules in a different repo?
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gitpod is more or less deprecated, so not sure you still need this file.
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I know it's deprecated, but it's still in the nf-core/modules repo. I did a wholesale copy (+ templating) without apply too much judgment on what is needed, valid, etc. I didn't want to implicitly review nf-core/modules through this.
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Here I've imported all files from the latest nf-core/modules repository.
In particular, it introduces a much better nf-test support, including sharding the test runs.
I also fixed a couple of variables in the copier template and changed the instructions to address #2