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Many thanks for taking an interest in improving CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing.
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Many thanks for taking an interest in improving nf-cmgg/preprocessing.
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We try to manage the required tasks for CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing using GitHub issues, you probably came to this page when creating one.
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We try to manage the required tasks for nf-cmgg/preprocessing using GitHub issues, you probably came to this page when creating one.
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Please use the pre-filled template to save time.
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However, don't be put off by this template - other more general issues and suggestions are welcome!
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Contributions to the code are even more welcome ;)
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## Contribution workflow
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If you'd like to write some code for CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing, the standard workflow is as follows:
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If you'd like to write some code for nf-cmgg/preprocessing, the standard workflow is as follows:
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1. Check that there isn't already an issue about your idea in the [CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing issues](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
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2.[Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing repository](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing) to your GitHub account
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1. Check that there isn't already an issue about your idea in the [nf-cmgg/preprocessing issues](https://github.com/nf-cmgg/preprocessing/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
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2.[Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-cmgg/preprocessing repository](https://github.com/nf-cmgg/preprocessing) to your GitHub account
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3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
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4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
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5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
@@ -23,6 +23,12 @@ If you're not used to this workflow with git, you can start with some [docs from
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## Tests
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You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
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```bash
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nf-test test --profile debug,test,docker --verbose
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```
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When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
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Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
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@@ -52,7 +58,7 @@ These tests are run both with the latest available version of `Nextflow` and als
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## Pipeline contribution conventions
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To make the CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
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To make the nf-cmgg/preprocessing code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
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### Adding a new step
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@@ -79,7 +85,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
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Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
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The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
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The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
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### Naming schemes
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To get started:
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- Open the repo in [Codespaces](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/codespaces)
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- Open the repo in [Codespaces](https://github.com/nf-cmgg/preprocessing/codespaces)
Many thanks for contributing to CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing!
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Many thanks for contributing to nf-cmgg/preprocessing!
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Please fill in the appropriate checklist below (delete whatever is not relevant).
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These are the most common things requested on pull requests (PRs).
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Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
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Learn more about contributing: [CONTRIBUTING.md](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/tree/master/.github/CONTRIBUTING.md)
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Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-cmgg/preprocessing/tree/master/.github/CONTRIBUTING.md)
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-->
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## PR checklist
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-[ ] This comment contains a description of changes (with reason).
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-[ ] If you've fixed a bug or added code that should be tested, add tests!
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-[ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/tree/master/.github/CONTRIBUTING.md)
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-[ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-cmgg/preprocessing/tree/master/.github/CONTRIBUTING.md)
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-[ ] Make sure your code lints (`nf-core lint`).
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-[ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
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-[ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
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-[ ] Usage Documentation in `docs/usage.md` is updated.
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-[ ] Output Documentation in `docs/output.md` is updated.
stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
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stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
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