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Contributing

Thank you for reading this guide and contributing to the workflow!

Table of Contents

Support

If you need any help getting started or solving an error:

  1. Read the documentation for the relevant section
  2. Check the issues trackers for similar problems and solutions
  3. Open an issue with one of the following labels:
    • help wanted for when extra attention is needed
    • question for when further information is requested

Feedback

If you have any suggestions or enhancements you would like:

  1. Read the documentation to confirm the feature is not available
  2. Search the issues tracker for similar suggestions and outcomes
  3. Open an issue with one of the following labels:
    • documentation for improvements or additions to documentation
    • enhancement for new features or requests

Testing

Run the workflow on the bundled test data using the command shown below:

$ snakemake --snakefile workflow/Snakefile --cores 4 --directory .test --show-failed-logs --use-conda --conda-cleanup-pkgs cache

You can also generate unit tests for your code:

$ snakemake --snakefile workflow/Snakefile --directory .test snakemake --generate-unit-tests

Linting

This project uses the Snakemake linter to analyse the workflow and highlight issues that should be solved in order to follow best practices. The linter can be invoked as shown below:

$ snakemake --lint

Contributions must pass all linting checks before a pull request will be considered.

Formatting

This project uses snakefmt to enforce a consistent coding style. Follow the instructions below to install and run the formatter on your Snakemake files:

Install snakefmt via conda:

$ conda install -c bioconda -n snakefmt snakefmt

Format a single file:

$ snakefmt Snakefile

Format multiple files:

$ snakefmt workflow/

Contributions must pass all formatting checks before a pull request will be considered.

Conduct

Contributors must adhere to our Code of Conduct and violations should be reported to James Ashmore as soon as possible.