Enhancing the nf-core/scdownstream pipeline with new analyses and modernization

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Goals

This project aims to further enhance the nf-core/scdownstream pipeline by implementing new analytical features and modernizing existing components.

By addressing open feature requests and technical debt, we aim to improve reproducibility, usability, and alignment with current single-cell best practices.

Contributors of intermediate and advanced experience levels are especially encouraged to participate.

Tasks

• Implement cell cycle analysis (issue #170)

  • Integrate standardized cell cycle scoring into the pipeline
  • Ensure compatibility with existing downstream modules

• Implement scDblFinder as a module (issue #144)

  • Add scDblFinder as an nf-core compliant module
  • Ensure proper container/Conda environment support

• Add sample sex prediction functionality (issue #171)

  • Implement automated sex prediction based on expression markers
  • Integrate outputs into summary reports

• Migrate legacy steps to use AnndataR (issue #207)

  • Replace older data handling steps with AnndataR-based workflows
  • Improve maintainability and future compatibility of the pipeline

• Update MAD-based dynamic filtering option PR to comply with latest nf-core template (PR #204)

  • Refactor open pull request to align with current nf-core pipeline standards
  • Ensure template compliance and successful CI checks