Run the pinned nf-core/scrnaseq pipeline with validated inputs and parameters.
npx skills add https://github.com/danilomonge/nf-claw --skill scrnaseq
Please help me install this Agent Skill. Skill: scrnaseq Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/scrnaseq Command: npx skills add https://github.com/danilomonge/nf-claw --skill scrnaseq
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.
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.
High-intent search queries and answers about installing and using this skill.
To run a single-cell RNA-seq pipeline, you launch the pinned nf-core/scrnaseq release by passing mandatory input and outdir arguments alongside your schema-checked samplesheet for validated, provenance-ready execution.
Single-cell RNA-seq data processing supports aligners including simpleaf, cellranger, cellrangermulti, cellrangerarc, star, and kallisto across common sample sheet-driven 10x Genomics workflow scenarios.
Yes, you can select specific nf-core/scrnaseq pipeline versions through release pinning, allowing you to lock behavior from a non-latest upstream release for reproducible analysis.
Input validation prevents malformed runs by applying a strict samplesheet schema and checking mandatory parameters, ensuring only correctly formatted single-cell RNA-seq inputs proceed to execution.
An scRNA-seq workflow run produces a complete results directory containing MultiQC reports and execution provenance, capturing run metadata and structured outputs for traceable analysis.
Executing the nf-core/scrnaseq workflow requires the Nextflow framework to run the pinned pipeline release and apply its schema-checked command-line flags for single-cell RNA-seq processing.
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