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Copy file name to clipboardexpand all lines: .github/CONTRIBUTING.md
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@@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/sarek, the standard workflow is as
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1. Check that there isn't already an issue about your idea in the [nf-core/sarek issues](https://github.com/nf-core/sarek/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-core/sarek repository](https://github.com/nf-core/sarek) 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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### 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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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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Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
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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 `${task.cpus}` and `${task.memory}` variables in the `script:` block.
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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]`
Copy file name to clipboardexpand all lines: .github/PULL_REQUEST_TEMPLATE.md
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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/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
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-[ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
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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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