Support & Contributions

Getting Help & Reporting Issues

We strive to make Epi-Flow as robust and user-friendly as possible, but issues can still arise. The best place to ask questions, report a bug, or request a feature is on our official GitHub Issues page.

Click here to open a new issue

Helping Us Help You

To resolve your issue as quickly as possible, a clear and informative bug report is essential. When you open an issue, please include the following information:

  1. A Descriptive Title: For example, “Pipeline fails during MACS3 step with ATAC-seq data” is much more helpful than “Script error.”

  2. The Exact Command: Copy and paste the full command you used to run epi_flow.sh.

  3. The Complete Error Message: Copy the full error message you saw in your terminal. Don’t summarize it; the exact wording is often crucial for debugging.

  4. The Relevant Log File: The pipeline creates log files for each step in the logs/ directory. If a specific tool failed (e.g., bowtie2), please attach the corresponding log file (e.g., bowtie2.log) to your issue.

  5. Your Environment: Briefly describe your setup. For example:

    • “Running in a Conda environment on Ubuntu 22.04.”

    • “Using HPC modules on a SLURM cluster.”

Providing this information helps us reproduce the error and find a solution much faster.

Thank you for helping to improve Epi-Flow!