scrnaseq

What problem does it solve?

This Skill removes the guesswork from running the nf-core/scrnaseq pipeline by turning a complex single-cell RNA-seq workflow into a validated, reproducible command sequence with the right inputs, parameters, and run targets.

Core Features & Use Cases

• Pipeline Execution: Launch the pinned nf-core/scrnaseq release for single-cell RNA-seq data processing.
• Input Validation: Use a strict samplesheet schema and required parameter checks to prevent malformed runs.
• Release-Aware Runs: Select specific pipeline versions when you need behavior from a non-latest upstream release.
• Provenance and Outputs: Capture run metadata, reports, and structured output directories for traceable analysis.
• Use Case: A bioinformatics analyst can process 10x Genomics data, choose an aligner such as simpleaf or cellranger, and produce a complete results directory with MultiQC and execution provenance.

Quick Start

Use the scrnaseq skill to run your single-cell RNA-seq samplesheet through the pinned nf-core/scrnaseq pipeline and save the results to the output directory you specify.