Skip to content

CONTRIBUTING.md

Latest commit

 

History

History
95 lines (60 loc) · 4.71 KB

CONTRIBUTING.md

File metadata and controls

95 lines (60 loc) · 4.71 KB
Raw

seqeralabs/nf-aggregate: Contributing Guidelines

Hi there! Many thanks for taking an interest in improving seqeralabs/nf-aggregate.

We try to manage the required tasks for seqeralabs/nf-aggregate using GitHub issues, you probably came to this page when creating one. Please use the pre-filled template to save time.

However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;)

Contribution workflow

If you'd like to write some code for seqeralabs/nf-aggregate, the standard workflow is as follows:

  1. Check that there isn't already an issue about your idea in the seqeralabs/nf-aggregate issues to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
  2. Fork the seqeralabs/nf-aggregate repository to your GitHub account
  3. Make the necessary changes / additions within your forked repository following Pipeline conventions
  4. Update nextflow_schema.json for any new or changed parameters.
  5. Submit a Pull Request against main and wait for the code to be reviewed and merged

If you're not used to this workflow with git, you can start with some docs from GitHub or even their excellent git resources.

Tests

When you create a pull request with changes, GitHub Actions will run automatic tests. Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.

Changelog and release notes

Release notes are drafted automatically from merged pull requests using GitHub labels.

  • Apply bug, enhancement, or documentation to have your PR included under the matching release notes section.
  • Apply renovate-actions for GitHub Actions and dependency-maintenance changes.
  • PRs without one of the release labels above are excluded from the automated changelog draft.
  • CHANGELOG.md is maintained at release time, so PR authors do not need to edit it for routine changes.

Patch

⚠️ Only in the unlikely and regretful event of a release happening with a bug.

  • On your own fork, make a new branch patch based on upstream/main or upstream/master.
  • Fix the bug, and bump version (X.Y.Z+1).
  • Open a pull-request from patch to main/master with the changes.

Pipeline contribution conventions

To make the seqeralabs/nf-aggregate 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.

Adding a new step

If you wish to contribute a new step, please use the following coding standards:

  1. Define the corresponding input channel into your new process from the expected previous process channel.
  2. Write the process block (see below).
  3. Define the output channel if needed (see below).
  4. Add any new parameters to nextflow.config with a default (see below).
  5. Add any new parameters to nextflow_schema.json with help text.
  6. Add sanity checks and validation for all relevant parameters.
  7. Perform local tests to validate that the new code works as expected.
  8. If applicable, add a new test in the tests directory.
  9. Update any user-facing docs touched by the change.

Default values

Parameters should be initialised / defined with default values within the params scope in nextflow.config.

Once there, update nextflow_schema.json to match.

Default processes resource requirements

Set sensible defaults for process CPUs, memory, and time close to the workflow or module that owns them.

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.

Naming schemes

Please use the following naming schemes, to make it easy to understand what is going where.

  • initial process channel: ch_output_from_<process>
  • intermediate and terminal channels: ch_<previousprocess>_for_<nextprocess>

GitHub Codespaces

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.

To get started:

  • Open the repo in Codespaces
  • Tools installed
    • Nextflow

Devcontainer specs: