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🎉 Transfer development version from dsp proteomics course to it's own repo
See for way from nf-core template to this point the commit in this PR - biosustain/dsp_course_proteomics_intro#18 Development will now continue here.
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‎.devcontainer/devcontainer.json‎

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{
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"name": "nfcore",
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"image": "nfcore/gitpod:latest",
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"remoteUser": "gitpod",
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"runArgs": ["--privileged"],
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// Configure tool-specific properties.
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"customizations": {
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// Configure properties specific to VS Code.
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"vscode": {
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// Set *default* container specific settings.json values on container create.
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"settings": {
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"python.defaultInterpreterPath": "/opt/conda/bin/python"
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},
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// Add the IDs of extensions you want installed when the container is created.
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"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
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}
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}
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}

‎.gitattributes‎

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*.config linguist-language=nextflow
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*.nf.test 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/proteomicsanalysis`: Contributing Guidelines
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Hi there!
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Many thanks for taking an interest in improving nf-core/proteomicsanalysis.
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We try to manage the required tasks for nf-core/proteomicsanalysis 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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> [!NOTE]
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> If you need help using or modifying nf-core/proteomicsanalysis then the best place to ask is on the nf-core Slack [#proteomicsanalysis](https://nfcore.slack.com/channels/proteomicsanalysis) 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/proteomicsanalysis, 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/proteomicsanalysis issues](https://github.com/nf-core/proteomicsanalysis/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/proteomicsanalysis repository](https://github.com/nf-core/proteomicsanalysis) 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 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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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 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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### 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/main` or `upstream/master`.
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- Fix the bug, and bump version (X.Y.Z+1).
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- Open a pull-request from `patch` to `main`/`master` with the changes.
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## Getting help
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For further information/help, please consult the [nf-core/proteomicsanalysis documentation](https://nf-co.re/proteomicsanalysis/usage) and don't hesitate to get in touch on the nf-core Slack [#proteomicsanalysis](https://nfcore.slack.com/channels/proteomicsanalysis) 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/proteomicsanalysis` 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 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 in the `tests` directory.
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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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### Default values
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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 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/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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### 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 pipelines 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).
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## GitHub Codespaces
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This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
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To get started:
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- Open the repo in [Codespaces](https://github.com/nf-core/proteomicsanalysis/codespaces)
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- Tools installed
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- nf-core
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- Nextflow
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Devcontainer specs:
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- [DevContainer config](.devcontainer/devcontainer.json)

‎.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/proteomicsanalysis pipeline documentation](https://nf-co.re/proteomicsanalysis/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. 23.04.0)_
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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, Charliecloud, or Apptainer)_
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* OS _(eg. CentOS Linux, macOS, Linux Mint)_
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* Version of nf-core/proteomicsanalysis _(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 #proteomicsanalysis channel"
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url: https://nfcore.slack.com/channels/proteomicsanalysis
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about: Discussion about the nf-core/proteomicsanalysis 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/proteomicsanalysis 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/proteomicsanalysis pull request
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Many thanks for contributing to nf-core/proteomicsanalysis!
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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/proteomicsanalysis/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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- [ ] 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/proteomicsanalysis/tree/master/.github/CONTRIBUTING.md)
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- [ ] If necessary, also make a PR on the nf-core/proteomicsanalysis _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 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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- [ ] `CHANGELOG.md` is updated.
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- [ ] `README.md` is updated (including new tool citations and authors/contributors).

‎.github/actions/get-shards/action.yml‎

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name: "Get number of shards"
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description: "Get the number of nf-test shards for the current CI job"
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inputs:
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max_shards:
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description: "Maximum number of shards allowed"
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required: true
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paths:
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description: "Component paths to test"
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required: false
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tags:
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description: "Tags to pass as argument for nf-test --tag parameter"
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required: false
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outputs:
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shard:
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description: "Array of shard numbers"
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value: ${{ steps.shards.outputs.shard }}
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total_shards:
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description: "Total number of shards"
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value: ${{ steps.shards.outputs.total_shards }}
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runs:
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using: "composite"
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steps:
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- name: Install nf-test
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uses: nf-core/setup-nf-test@v1
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with:
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version: ${{ env.NFT_VER }}
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- name: Get number of shards
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id: shards
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shell: bash
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run: |
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# Run nf-test with dynamic parameter
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nftest_output=$(nf-test test \
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--profile +docker \
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$(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
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--dry-run \
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--ci \
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--changed-since HEAD^) || {
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echo "nf-test command failed with exit code $?"
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echo "Full output: $nftest_output"
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exit 1
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}
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echo "nf-test dry-run output: $nftest_output"
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# Default values for shard and total_shards
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shard="[]"
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total_shards=0
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# Check if there are related tests
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if echo "$nftest_output" | grep -q 'No tests to execute'; then
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echo "No related tests found."
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else
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# Extract the number of related tests
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number_of_shards=$(echo "$nftest_output" | sed -n 's|.*Executed \([0-9]*\) tests.*|\1|p')
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if [[ -n "$number_of_shards" && "$number_of_shards" -gt 0 ]]; then
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shards_to_run=$(( $number_of_shards < ${{ inputs.max_shards }} ? $number_of_shards : ${{ inputs.max_shards }} ))
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shard=$(seq 1 "$shards_to_run" | jq -R . | jq -c -s .)
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total_shards="$shards_to_run"
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else
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echo "Unexpected output format. Falling back to default values."
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fi
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fi
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# Write to GitHub Actions outputs
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echo "shard=$shard" >> $GITHUB_OUTPUT
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echo "total_shards=$total_shards" >> $GITHUB_OUTPUT
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# Debugging output
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echo "Final shard array: $shard"
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echo "Total number of shards: $total_shards"

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