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initial template build from nf-core/tools, version 2.3.dev0
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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
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modules/nf-core/** linguist-generated
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subworkflows/nf-core/** linguist-generated

‎.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/proteinfold: Contributing Guidelines
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Hi there!
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Many thanks for taking an interest in improving nf-core/proteinfold.
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We try to manage the required tasks for nf-core/proteinfold 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/proteinfold then the best place to ask is on the nf-core Slack [#proteinfold](https://nfcore.slack.com/channels/proteinfold) 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/proteinfold, 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/proteinfold issues](https://github.com/nf-core/proteinfold/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/proteinfold repository](https://github.com/nf-core/proteinfold) 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/proteinfold documentation](https://nf-co.re/proteinfold/usage) and don't hesitate to get in touch on the nf-core Slack [#proteinfold](https://nfcore.slack.com/channels/proteinfold) 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/proteinfold 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 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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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.yaml` 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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### 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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### 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.yml

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name: Bug report
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description: Report something that is broken or incorrect
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labels: bug
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body:
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- type: markdown
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attributes:
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value: |
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Before you post this issue, please check the documentation:
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- [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
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- [nf-core/proteinfold pipeline documentation](https://nf-co.re/proteinfold/usage)
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- type: textarea
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id: description
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attributes:
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label: Description of the bug
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description: A clear and concise description of what the bug is.
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validations:
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required: true
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- type: textarea
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id: command_used
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attributes:
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label: Command used and terminal output
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description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
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render: console
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placeholder: |
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$ nextflow run ...
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Some output where something broke
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- type: textarea
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id: files
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attributes:
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label: Relevant files
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description: |
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Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
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Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
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- type: textarea
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id: system
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attributes:
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label: System information
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description: |
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* Nextflow version _(eg. 21.10.3)_
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* Hardware _(eg. HPC, Desktop, Cloud)_
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* Executor _(eg. slurm, local, awsbatch)_
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* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
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* OS _(eg. CentOS Linux, macOS, Linux Mint)_
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* Version of nf-core/proteinfold _(eg. 1.1, 1.5, 1.8.2)_

‎.github/ISSUE_TEMPLATE/config.yml

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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 #proteinfold channel"
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url: https://nfcore.slack.com/channels/proteinfold
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about: Discussion about the nf-core/proteinfold pipeline

‎.github/ISSUE_TEMPLATE/feature_request.yml

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name: Feature request
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description: Suggest an idea for the nf-core/proteinfold pipeline
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labels: enhancement
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body:
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- type: textarea
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id: description
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attributes:
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label: Description of feature
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description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
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validations:
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required: true

‎.github/PULL_REQUEST_TEMPLATE.md

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<!--
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# nf-core/proteinfold pull request
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Many thanks for contributing to nf-core/proteinfold!
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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/nf-core/proteinfold/tree/master/.github/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/proteinfold/tree/master/.github/CONTRIBUTING.md)
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- [ ] If necessary, also make a PR on the nf-core/proteinfold _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/proteinfold'
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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@v3
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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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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/proteinfold/work-${{ github.sha }}
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parameters: |
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{
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/proteinfold/results-${{ github.sha }}"
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}
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profiles: test_full,aws_tower
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nextflow_config: |
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process.errorStrategy = 'retry'
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process.maxRetries = 3

‎.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/proteinfold'
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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@v3
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/proteinfold/work-${{ github.sha }}
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parameters: |
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{
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/proteinfold/results-test-${{ github.sha }}"
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}
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profiles: test,aws_tower
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nextflow_config: |
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process.errorStrategy = 'retry'
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process.maxRetries = 3

‎.github/workflows/branch.yml

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name: nf-core branch protection
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# This workflow is triggered on PRs to master branch on the repository
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# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
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on:
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pull_request_target:
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branches: [master]
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jobs:
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test:
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runs-on: ubuntu-latest
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steps:
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# PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
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- name: Check PRs
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if: github.repository == 'nf-core/proteinfold'
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run: |
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{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/proteinfold ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
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# If the above check failed, post a comment on the PR explaining the failure
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# NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
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- name: Post PR comment
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if: failure()
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uses: mshick/add-pr-comment@v1
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with:
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message: |
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## This PR is against the `master` branch :x:
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* Do not close this PR
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* Click _Edit_ and change the `base` to `dev`
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* This CI test will remain failed until you push a new commit
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---
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Hi @${{ github.event.pull_request.user.login }},
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It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
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The `master` branch on nf-core repositories should always contain code from the latest release.
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Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
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You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
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Note that even after this, the test will continue to show as failing until you push a new commit.
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Thanks again for your contribution!
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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allow-repeats: false
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