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Nanopype is a growing open source project for nanopore sequencing data processing. While we continuously improve and expand the pipeline external contributions are always welcome and appreciated.


These are mostly guidelines, not rules. Use your best judgment and most importantly: There's nothing you can do wrong 1.

Reporting Bugs

Before submitting a Bug Report
  • Check in our Release Notes, if you're running the most recent version of Nanopype and if the bug you encounter was already mentioned here. Consider updating, if a new version is available.
  • (Re-)Run the module tests for your installation. Also automated on Travis-CI, the tests help us to distinguish between problems caused by the local environment, the input data or by the pipeline implementation.
  • Search the github issues to see if the problem was already reported. If it has and the issue is open, leave a comment instead of opening a new one.

Submitting a (good) Bug Report

Explain the problem and include additional details to help maintainers reproduce the problem:
  • Use one of the provided templates if appropriate.
  • Use a clear and descriptive title.
  • Describe the exact steps which reproduce the problem with as many details as possible.
  • Describe the behavior you observed and what exactly is the problem with that.
  • Describe the behavior you expected to see instead.
  • If the problem is related to the cluster execution, does it occur when running locally?
  • Attach any log files and full command line output as (zipped) text files.
Include details about your configuration and environment:
  • Which version of Nanopype are you using?
  • Which of the installation methods are you using?
  • What is your operating system?
  • Which changes to the nanopype.yaml and env.yaml have you made?

Suggesting Enhancements

Submitting a (good) Enhancement Suggestion
  • Use a clear and descriptive title for the issue.
  • Provide a step-by-step description of the suggested enhancement in as many details as possible.
  • Describe the current behavior and explain which behavior you expected to see instead and why.
  • Explain why this enhancement would be useful to more Nanopype users

Writing Your Contribution

Unsure where to begin? Look for issues labeled as good first issue or help wanted and articulate you wish to help.

Already a pro? Fork the repository, suggest your enhancement with an issue and start coding.

The following guide aims to keep up Nanopype's quality and provide a stable pipeline.
  • Follow the coding style of python and snakemake files
  • If you add new files include the copyright and license header. Complete the contents, description and restrictions fields.
  • Use descriptive commit messages and group functional changes into individual commits.
  • Reference pull requests or issues after the commit title

Finally consider a rebase and create a pull-request for your feature branch against the Nanopype development branch.


A big thank you to everyone writing code for Nanopype:

  • Sara Hetzel (sarahet)
  • Miguel Machado (miguelpmachado)

  1. Our contribution guidelines are inspired by the ones from Atom