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Many thanks for taking an interest in improving sanger-tol/genomeassembly.
@@ -16,13 +16,19 @@ If you'd like to write some code for sanger-tol/genomeassembly, the standard wor
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1. Check that there isn't already an issue about your idea in the [sanger-tol/genomeassembly issues](https://github.com/sanger-tol/genomeassembly/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 [sanger-tol/genomeassembly repository](https://github.com/sanger-tol/genomeassembly) 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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4. Use `nf-core pipelines 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
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If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
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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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@@ -31,7 +37,7 @@ There are typically two types of tests that run:
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### Lint tests
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`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
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To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
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To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint <pipeline-directory>` command.
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If any failures or warnings are encountered, please follow the listed URL for more documentation.
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:warning: Only in the unlikely and regretful event of a release happening with a bug.
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- On your own fork, make a new branch `patch` based on `upstream/master`.
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- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`.
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- Fix the bug, and bump version (X.Y.Z+1).
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-A PR should be made on `master`from patch to directly this particular bug.
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-Open a pull-request from `patch` to `main`/`master`with the changes.
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## Pipeline contribution conventions
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To make the sanger-tol/genomeassembly 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 `sanger-tol/genomeassembly` 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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If you wish to contribute a new step, please use the following coding standards:
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1. Define the corresponding input channel into your new process from the expected previous process channel
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1. Define the corresponding input channel into your new process from the expected previous process channel.
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2. Write the process block (see below).
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3. Define the output channel if needed (see below).
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4. Add any new parameters to `nextflow.config` with a default (see below).
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5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
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5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
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6. Add sanity checks and validation for all relevant parameters.
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7. Perform local tests to validate that the new code works as expected.
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8. If applicable, add a new test command in `.github/workflow/ci.yml`.
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9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
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10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
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8. If applicable, add a new test in the `tests` directory.
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### Default values
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Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
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Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.
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Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
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Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
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### Default processes resource requirements
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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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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/main/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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### Nextflow version bumping
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If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
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If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]`
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@@ -16,8 +16,9 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/sanger-tol/g
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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/sanger-tol/genomeassembly/tree/master/.github/CONTRIBUTING.md)
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-[ ] Make sure your code lints (`nf-core lint`).
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-[ ] Make sure your code lints (`nf-core pipelines 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.
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