nf-core/scrnaseq

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Contribute to nf-core/scrnaseq pipeline.

Goal

We aim to extend the nf-core/scrnaseq pipeline with functionality for RNA velocity calculation, sample aggregation, and alternative chemistries.

Tasks

1. Integrate the existing velocyto module for RNA velocity calculation from Cell Ranger .bam files.
2. Create cellranger_aggr and cellrangermulti_aggr modules to support Cell Ranger aggregation workflow.
3. Assess the feasibility of integrating the BD Rhapsody processing pipeline and, if viable, create a module for it. Intro · Manual
4. Assess the feasibility of integrating cell type annotation options and, if viable, create the necessary module or subworkflow. (matching 10X cellranger annotate)

Location

Participants can join in person at Helmholtz Munich or online.

Contributors of all experience levels are welcome; familiarity with Nextflow is helpful.