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‎.editorconfig

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root = true
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[*]
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charset = utf-8
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end_of_line = lf
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insert_final_newline = true
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trim_trailing_whitespace = true
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indent_size = 4
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indent_style = space
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[*.{yml,yaml}]
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indent_size = 2
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[*.json]
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insert_final_newline = unset
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# These files are edited and tested upstream in nf-core/modules
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[/modules/nf-core/**]
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charset = unset
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end_of_line = unset
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insert_final_newline = unset
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trim_trailing_whitespace = unset
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indent_style = unset
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indent_size = unset
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[/assets/email*]
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indent_size = unset

‎.gitattributes

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*.config linguist-language=nextflow

‎.github/.dockstore.yml

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# Dockstore config version, not pipeline version
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version: 1.2
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workflows:
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- subclass: nfl
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primaryDescriptorPath: /nextflow.config
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publish: True

‎.github/CONTRIBUTING.md

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# nf-core/bpertussisciwgs: Contributing Guidelines
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Hi there!
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Many thanks for taking an interest in improving nf-core/bpertussisciwgs.
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We try to manage the required tasks for nf-core/bpertussisciwgs 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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> If you need help using or modifying nf-core/bpertussisciwgs then the best place to ask is on the nf-core Slack [#bpertussisciwgs](https://nfcore.slack.com/channels/bpertussisciwgs) channel ([join our Slack here](https://nf-co.re/join/slack)).
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## Contribution workflow
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If you'd like to write some code for nf-core/bpertussisciwgs, the standard workflow is as follows:
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1. Check that there isn't already an issue about your idea in the [nf-core/bpertussisciwgs issues](https://github.com/nf-core/bpertussisciwgs/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/bpertussisciwgs repository](https://github.com/nf-core/bpertussisciwgs) 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
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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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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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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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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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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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If there are any failures then the automated tests fail.
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These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code.
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## Patch
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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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* 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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## Getting help
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For further information/help, please consult the [nf-core/bpertussisciwgs documentation](https://nf-co.re/bpertussisciwgs/usage) and don't hesitate to get in touch on the nf-core Slack [#bpertussisciwgs](https://nfcore.slack.com/channels/bpertussisciwgs) channel ([join our Slack here](https://nf-co.re/join/slack)).
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## Pipeline contribution conventions
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To make the nf-core/bpertussisciwgs 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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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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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.yml`.
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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. 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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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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### 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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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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### 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:
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```bash
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<YOUR_TOOL> --version &> v_<YOUR_TOOL>.txt 2>&1 || true
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```
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or
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```bash
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<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).

‎.github/ISSUE_TEMPLATE/bug_report.md

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---
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name: Bug report
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about: Report something that is broken or incorrect
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labels: bug
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---
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<!--
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# nf-core/bpertussisciwgs bug report
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Hi there!
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Thanks for telling us about a problem with the pipeline.
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Please delete this text and anything that's not relevant from the template below:
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-->
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## Check Documentation
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I have checked the following places for your error:
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- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
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- [ ] [bpertussisciwgs pipeline documentation](https://github.com/cdcgov/bpertussis-ciwgs/usage)
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## Description of the bug
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<!-- A clear and concise description of what the bug is. -->
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## Steps to reproduce
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Steps to reproduce the behaviour:
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1. Command line: <!-- [e.g. `nextflow run ...`] -->
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2. See error: <!-- [Please provide your error message] -->
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## Expected behaviour
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<!-- A clear and concise description of what you expected to happen. -->
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## Log files
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Have you provided the following extra information/files:
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- [ ] The command used to run the pipeline
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- [ ] The `.nextflow.log` file <!-- this is a hidden file in the directory where you launched the pipeline -->
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## System
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- Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->
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- Executor: <!-- [e.g. slurm, local, awsbatch...] -->
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- OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] -->
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- Version <!-- [e.g. 7, 10.13.6, 18.3...] -->
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## Nextflow Installation
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- Version: <!-- [e.g. 21.04.0] -->
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## Container engine
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- Engine: <!-- [e.g. Conda, Docker, Singularity, Podman, Shifter or Charliecloud] -->
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- version: <!-- [e.g. 1.0.0] -->
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## Additional context
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<!-- Add any other context about the problem here. -->

‎.github/ISSUE_TEMPLATE/config.yml

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blank_issues_enabled: false
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contact_links:
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- name: Join nf-core
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url: https://nf-co.re/join
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about: Please join the nf-core community here
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- name: "Slack #bpertussisciwgs channel"
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url: https://nfcore.slack.com/channels/bpertussisciwgs
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about: Discussion about the nf-core/bpertussisciwgs pipeline

‎.github/ISSUE_TEMPLATE/feature_request.md

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---
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name: Feature request
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about: Suggest an idea for the bpertussisciwgs pipeline
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labels: enhancement
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---
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<!--
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# bpertussisciwgs feature request
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Hi there!
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Thanks for suggesting a new feature for the pipeline!
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Please delete this text and anything that's not relevant from the template below:
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-->
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## Is your feature request related to a problem? Please describe
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<!-- A clear and concise description of what the problem is. -->
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<!-- e.g. [I'm always frustrated when ...] -->
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## Describe the solution you'd like
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<!-- A clear and concise description of what you want to happen. -->
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## Describe alternatives you've considered
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<!-- A clear and concise description of any alternative solutions or features you've considered. -->
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## Additional context
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<!-- Add any other context about the feature request here. -->

‎.github/PULL_REQUEST_TEMPLATE.md

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<!--
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# bpertussisciwgs pull request
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Many thanks for contributing to bpertussisciwgs!
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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/cdcgov/bpertussisciwgs/tree/master/CONTRIBUTING.md)
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-->
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<!-- markdownlint-disable ul-indent -->
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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/nf-core/bpertussisciwgs/tree/master/.github/CONTRIBUTING.md)
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- [ ] If necessary, also make a PR on the nf-core/bpertussisciwgs _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).

‎.github/workflows/awsfulltest.yml

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name: nf-core AWS full size tests
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# This workflow is triggered on published releases.
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# It can be additionally triggered manually with GitHub actions workflow dispatch button.
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# It runs the -profile 'test_full' on AWS batch
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on:
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release:
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types: [published]
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workflow_dispatch:
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jobs:
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run-tower:
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name: Run AWS full tests
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if: github.repository == 'nf-core/bpertussisciwgs'
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runs-on: ubuntu-latest
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steps:
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- name: Launch workflow via tower
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uses: nf-core/tower-action@master
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# TODO nf-core: You can customise AWS full pipeline tests as required
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# Add full size test data (but still relatively small datasets for few samples)
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# on the `test_full.config` test runs with only one set of parameters
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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pipeline: ${{ github.repository }}
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revision: ${{ github.sha }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/bpertussisciwgs/work-${{ github.sha }}
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parameters: |
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{
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bpertussisciwgs/results-${{ github.sha }}"
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}
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profiles: '[ "test_full", "aws_tower" ]'
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‎.github/workflows/awstest.yml

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name: nf-core AWS test
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# This workflow can be triggered manually with the GitHub actions workflow dispatch button.
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# It runs the -profile 'test' on AWS batch
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on:
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workflow_dispatch:
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jobs:
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run-tower:
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name: Run AWS tests
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if: github.repository == 'nf-core/bpertussisciwgs'
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runs-on: ubuntu-latest
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steps:
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- name: Launch workflow via tower
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uses: nf-core/tower-action@master
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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pipeline: ${{ github.repository }}
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revision: ${{ github.sha }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/bpertussisciwgs/work-${{ github.sha }}
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parameters: |
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{
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bpertussisciwgs/results-${{ github.sha }}"
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}
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profiles: '[ "test", "aws_tower" ]'
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