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@@ -18,8 +18,8 @@ If you'd like to write some code for nf-core/eager, 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/eager issues](https://github.com/nf-core/eager/issues) to avoid duplicating work
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* 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/eager repository](https://github.com/nf-core/eager) to your GitHub account
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3. Make the necessary changes / additions within your forked repository (following [code contribution guidelines](https://github.com/nf-core/eager/blob/dev/.github/CONTRIBUTING.md))
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4. Use `nf-core schema build .` and add any new parameters to the pipeline JSON schema (requires nf-core tools >= 1.10).
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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
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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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There are typically two types of tests that run:
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### Lint Tests
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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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If any failures or warnings are encountered, please follow the listed URL for more documentation.
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### Pipeline Tests
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### Pipeline tests
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Each `nf-core` pipeline should be set up with a minimal set of test-data.
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`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
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## Getting help
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For further information/help, please consult the [nf-core/eager documentation](https://nf-co.re/eager/latest/usage) and don't hesitate to get in touch on the nf-core Slack [#eager](https://nfcore.slack.com/channels/eager) channel ([join our Slack here](https://nf-co.re/join/slack)).
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For further information/help, please consult the [nf-core/eager documentation](https://nf-co.re/eager/usage) and don't hesitate to get in touch on the nf-core Slack [#eager](https://nfcore.slack.com/channels/eager) channel ([join our Slack here](https://nf-co.re/join/slack)).
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#Code Contribution Guidelines
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## Pipeline contribution conventions
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To make the EAGER2 code and processing logic more understandable for new contributors, and to ensure quality. We are making an attempt to somewhat-standardise the way the code is written.
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To make the nf-core/eager 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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If you wish to contribute a new module, please use the following coding standards.
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### Adding a new step
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The typical workflow for adding a new module is as follows:
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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 (or re-routing block, see below).
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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 flags/options to `nextflow.config` with a default (see below).
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5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build .`)
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5. Add any new flags/options to `nextflow_schema.json`**with help text** (with `nf-core schema build .`)
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6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter).
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7. Add sanity checks for all relevant parameters.
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8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
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9. Do local tests that the new code works properly and as expected.
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10. Add a new test command in `.github/workflow/ci.yaml`.
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11. If applicable add a [MultiQC](https://https://multiqc.info/) module.
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12. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.
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13. Add new flags/options to 'usage' documentation under `docs/usage.md`.
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14. Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
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13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
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## Default Values
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###Default values
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Default values should go in `nextflow.config` under the `params` scope, and `nextflow_schema.json` (latter with `nf-core schema build .`)
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Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
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## Default resource processes
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Once there, use `nf-core schema build .` to add to `nextflow_schema.json`.
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Defining recommended 'minimum' resource requirements (CPUs/Memory) for a process should be defined in `conf/base.config`. This can be utilised within the process using `${task.cpu}` or `${task.memory}` variables in the `script:` block.
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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/%7B%7Bcookiecutter.name_noslash%7D%7D/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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:warning: Note that in nf-core/eager we currently have our own custom process labels, so please check `base.config`!
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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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### Naming schemes
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Please use the following naming schemes, to make it easy to understand what is going where.
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* initial process channel: `ch_output_from_<process>`
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* intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
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* skipped process output: `ch_<previousstage>_for_<skipprocess>`(this goes out of the bypass statement described above)
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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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### Software version reporting
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If you add a new tool to the pipeline, please ensure you add the information of the tool to the `get_software_version` process.
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Add to the script block of the process, something like the following:
<YOUR_TOOL> --help | head -n 1 &> v_<YOUR_TOOL>.txt 2>&1||true
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```
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You then need to edit the script `bin/scrape_software_versions.py` to:
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1. Add a Python regex for your tool's `--version` output (as in stored in the `v_<YOUR_TOOL>.txt` file), to ensure the version is reported as a `v` and the version number e.g. `v2.1.1`
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2. Add a HTML entry to the `OrderedDict` for formatting in MultiQC.
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### Images and figures
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For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
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For all internal nf-core/eager documentation images we are using the 'Kalam' font by the Indian Type Foundry and licensed under the Open Font License. It can be found for download here [here](https://fonts.google.com/specimen/Kalam).
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## Process Concept
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}
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```
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## Naming Schemes
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Please use the following naming schemes, to make it easy to understand what is going where.
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* process output: `ch_output_from_<process>`(this should always go into the bypass statement described above).
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* skipped process output: `ch_<previousstage>_for_<skipprocess>`(this goes out of the bypass statement described above)
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* process inputs: `ch_<previousstage>_for_<process>` (this goes into a process)
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## Nextflow Version Bumping
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If you have agreement from reviewers, you may bump the 'default' minimum version of nextflow (e.g. for testing), with `nf-core bump-version`.
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## Software Version Reporting
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If you add a new tool to the pipeline, please ensure you add the information of the tool to the `get_software_version` process.
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Add to the script block of the process, something like the following:
<YOUR_TOOL> --help | head -n 1 &> v_<YOUR_TOOL>.txt 2>&1||true
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```
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You then need to edit the script `bin/scrape_software_versions.py` to
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1. add a (python) regex for your tools --version output (as in stored in the `v_<YOUR_TOOL>.txt` file), to ensure the version is reported as a `v` and the version number e.g. `v2.1.1`
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2. add a HTML block entry to the `OrderedDict` for formatting in MultiQC.
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> If a tool does not unfortunately offer any printing of version data, you may add this 'manually' e.g. with `echo "v1.1" > v_<YOUR_TOOL>.txt`
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## Images and Figures
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For all internal nf-core/eager documentation images we are using the 'Kalam' font by the Indian Type Foundry and licensed under the Open Font License. It can be found for download here [here](https://fonts.google.com/specimen/Kalam).
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For the overview image we follow the nf-core [style guidelines](https://nf-co.re/developers/design_guidelines).
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/nf-core/eager/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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-[ ] 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 necessary, also make a PR on the [nf-core/eager branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/nf-core/eager)
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-[ ] Ensure the test suite passes (`nextflow run . -profile test,docker --paired_end`).
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-[ ] Make sure your code lints ([`nf-core lint .`](https://nf-co.re/tools)).
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-[ ] Documentation in `docs` is updated
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-[ ]`CHANGELOG.md` is updated
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-[ ]`README.md` is updated
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**Learn more about contributing:**[CONTRIBUTING.md](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
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-[ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py`
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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/eager/tree/master/.github/CONTRIBUTING.md)
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-[ ] If necessary, also make a PR on the nf-core/eager _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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-[ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
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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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-[ ]`CHANGELOG.md` is updated.
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-[ ]`README.md` is updated (including new tool citations and authors/contributors).
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