Sustainability & Reproducibility

To ensure sustainable development, implicit documentation, and reproducibility each {module} has to fulfill the following requirements:

• GitHub repository for development and version control.
  • Descriptive name (i.e., what it does and its purpose e.g, dea_limma) using Snakecase i.e., split by underscores _.
  • README according to the provided template.
  • Repository structure according to Snakemake's best practice.
  • Releases (i.e., versions) according to the semantic versioning scheme.
  • Workflow rulegraph in workflow/dags/rulegraph.svg

    snakemake --rulegraph --forceall | dot -Tsvg > workflow/dags/rulegraph.svg

  • GitHub page displaying the README.
  • LICENSE file (recommendation: MIT).
  • CITATION.cff file.
    • CFF docs.
    • GitHub citation files.
    • Generator.
  • (Optional, but recommended) Add example data and configurations for users as a starting point.
  • (Optional, but recommended) Provide resources and/or external data sources (e.g., reference data) as links, or Zenodo, or Git Large File Storage.
• Zenodo repository to ensure compatibility, citability, and long-term archiving.
  • via automated GitHub hook
  • every GitHub release will trigger the creation of a new release in the Zenodo repository, and thereby a new DOI
  • the Zenodo repository will be annotated using the provided information in the CITATION.cff file in your GitHub repository
  • there is one permanent DOI that can be used to reference/cite all releases/versions of a given repository. We recommend using this DOI and the release version for referencing e.g., in publications
  • add the dynamic DOI badge to the GitHub repository
  • add the permanent project DOI to the README in the introduction, in the methods, at the bottom (Zenodo link), and to the CITATION.cff.
• Snakemake Workflow Catalog entry to increase visibility and findability.
  • increase visibility by fulfilling the requirements for Standardized Usage
  • every GitHub release will trigger the entry to be updated
• Snakemake Report for implicit documentation and collaboration
  • following the specified Report structure to enhance reproducibility (via export of used software and configuration) and ensure module compatibility
• Result directory
  • following the specified Result structure to enhance reproducibility (via export of used software and configuration) and ensure module compatibility
• Software Management with conda for reproducibility and portability.
  • specify the version of every entry in your conda environment specification files (workflow/envs/*.yaml)
• (COMING SOON) Containerization with Docker/Singularity for OS-level virtualization
  • this final virtualization frontier is to be explored and implemented across all MR.PARETO modules
  • automated containerization has been supported since Snakemake 6.0.0 (released 2021-02-26)
• Finally, add the {module} to the summary table with all modules in this repository's README under Modules.

Checklist

• GitHub repository with README, LICENSE, CITATION.cff, Snakemake Workflow Catalog entry, conda YAMLspecifications with exact versions.
• Zenodo repository via GitHub webhook.
• GitHub release to trigger Zenodo DOI generation.
• Add general and version-specific DOI to the GitHub README, CITATION.cff and MR.PARETO Modules.
• Final GitHub release with minor version bump including generated DOI.