nf-core/spatialaxe

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Project Aim

nf-core/spatialaxe is a bioinformatics best-practice processing and quality control pipeline for Xenium (and soon Atera) data. The pipeline is under active development and changes might occur frequently.

During the hackathon we want to solve existing issues including bugs, enhancements, and documentation.

Contribution Tracks

Depending on your level of experience with Nextflow and spatial omics, you can choose from different contribution tracks:

Quality Control Subworkflow (Beginner)

There are several open issues related to the quality control (QC) subworkflow of spatialaxe. Contributions may include implementing new modules, fixing existing bugs, and extending or improving current modules. This track is particularly suitable for contributors who are relatively new to Nextflow or spatial omics and would like to become familiar with the pipeline.

Documentation (Advanced Spatial Transcriptomics)

We are currently expanding the spatialaxe documentation, particularly in the areas of segmentation, quality control, and metadata handling. Contributions to this track involve applying the pipeline to different datasets, evaluating the results, and documenting findings and recommendations for specific use cases. This track is best suited for contributors with a solid understanding of spatial transcriptomics.

General Pipeline Functionality (Advanced Spatial Transcriptomics & Nextflow)

There are also several open issues related to the overall functionality of the spatialaxe pipeline, including bug fixes, enhancements, and improvements to existing features. This track is intended for contributors with experience in both spatial transcriptomics and Nextflow who are comfortable working on more complex pipeline-level challenges.