This project focuses on improving nf-core/scalpel, a nf-core pipeline for large omics data with single-cell data, isoform-aware quantification, and downstream analysis. SCALPEL was previously developed as a standalone Nextflow pipeline and the associated work was published in Nature Communications (2025). The current effort consists of reimplementing SCALPEL as a fully fledged nf-core pipeline so that it can be more easily deployed, maintained, and extended while integrating important updates into the workflow.
The Boston hackathon is a great opportunity to expand the pipeline scope, improve reliability, and make it easier for new contributors to get involved.
Goal
By the end of the hackathon, we want to make clear progress towards a more robust and release-ready nf-core implementation of SCALPEL, with broader support for different single-cell input technologies and stronger downstream analysis capabilities.
Planned tasks
- Integrate support for processing either 10x Chromium, Drop-seq, and potentially additional single-cell input formats.
- Work on nf-tests to improve coverage, reproducibility, and confidence in pipeline behavior.
- Set up sensible default configurations and container definitions for easier deployment.
- Integrate downstream single-cell analysis steps into the Nextflow execution.
- Add clearer error and warning messages for common or specific user-facing issues.
- Improve documentation and usage examples.
Who should join?
This project is a good fit for people interested in:
- working on a complex Nextflow pipeline for large omics data processing, particularly single-cell data for isoform quantification
- developing pipelines to process different types of omics input files
- pipeline testing, reproducibility, and nf-test
- R or Nextflow-based downstream analysis development
Recommended preparation
Participants will benefit from:
- Basic familiarity with Git and GitHub
- Some exposure to Nextflow or nf-core
- An interest in testing, debugging, or improving documentation
