rnaseq

What problem does it solve?

This Skill turns the complex nf-core rnaseq pipeline into a guided, reliable workflow for RNA sequencing analysis, reducing guesswork around inputs, flags, and release-specific behavior.

Core Features & Use Cases

• Runs the pinned nf-core rnaseq release with discovery-ready documentation for inputs, required parameters, optional controls, and outputs.
• Supports common RNA-seq scenarios including FASTQ-based analysis, pre-aligned BAM inputs, trimming, alignment or pseudoalignment, QC, quantification, contamination screening, and UMI handling.
• Helps users avoid invalid parameter combinations by surfacing schema-backed constraints, allowed values, and version-aware pipeline details.
• Useful for researchers and bioinformatics teams who need reproducible transcriptomics analysis with clear run instructions and standardized provenance.

Quick Start

Ask the Skill to run an nf-core rnaseq analysis for your samplesheet and output directory, then it will guide the correct parameters for the selected pipeline version.