🤝 Contributing to Cecret

September 7, 2026 · View on GitHub

We welcome contributions to the Cecret Nextflow workflow from the community! By participating in this project, you agree to abide by our Code of Conduct.

❓ How to Contribute

There are several ways you can help improve Cecret:

  1. Report a Bug: Find an issue or error in the pipeline.
  2. Suggest an Enhancement: Propose a new feature, a new organism workflow, or an updated tool version.
  3. Improve Documentation: Fix typos, clarify usage, or add new tutorials.
  4. Submit Code Changes (Pull Request): Write and submit code to fix a bug or implement a feature.

🐛 Reporting Bugs

Before reporting a bug, please search existing issues to see if the problem has already been addressed.

When submitting a new bug report via a GitHub Issue, please include the following critical information:

  • Cecret Version: The specific Git tag or commit hash you are using (e.g., v1.5.0 or main branch).
  • Execution Profile: The Nextflow profile used (e.g., -profile docker, -profile singularity).
  • Operating System/Environment: (e.g., Ubuntu 22.04, HPC Slurm cluster).
  • The Exact Error: Copy and paste the complete traceback or error message.
  • Nextflow Log: Attach or paste the content of the .nextflow.log file.
  • Reproduction Steps: Provide the minimal nextflow run command and any necessary input files (or links to public accessions) that can reliably recreate the bug.

✨ Suggesting Enhancements

If you have an idea for a new feature or an improvement to an existing process:

  • Use the GitHub Issues page and clearly label the issue as a "Feature Request."
  • Describe the goal of the feature and why it would be beneficial to the Cecret community.
  • Outline how the feature should be implemented, particularly if it involves adding new parameters, tools, or configuration files.

💻 Code Contribution Guidelines

We use the standard GitHub fork and pull request workflow.

Setup and Workflow

  1. Fork the repository to your personal GitHub account.
  2. Clone your fork locally: git clone git@github.com:YOUR-USERNAME/Cecret.git
  3. Create a dedicated branch for your contribution: git checkout -b fix/issue-123-bug or feature/add-new-tool.
  4. Install dependencies and run a minimal test of the pipeline locally before coding to ensure your environment is set up correctly.

Coding Standards

  • Nextflow/Groovy: Follow standard Groovy syntax and the conventions established in main.nf and the project's modules.
  • Containerization: All new processes must be containerized. Ensure your changes reference a public Docker/Singularity image (ideally from StaPHB or a reputable source).

Submitting a Pull Request (PR)

  1. Push your changes to your fork: git push origin YOUR-BRANCH-NAME
  2. Open a Pull Request targeting the main branch of the UPHL-BioNGS/Cecret repository.
  3. In the PR description, provide:
    • A clear title summarizing the change.
    • A detailed description of what you changed and why.
    • A reference to the original issue it addresses (e.g., "Closes #123").
    • A note confirming that you have tested the change.

🏛️ Code of Conduct

Please note that this project is governed by a Code of Conduct. By participating, you are expected to uphold this code. Please report unacceptable behavior to eriny@utah.gov.