What problem does it solve?
Epigenomics experiments span multiple assay types (ATAC-seq, ChIP-seq, CUT&RUN, CUT&Tag), each requiring different pipelines, controls, and peak-calling strategies. This Skill removes the guesswork of choosing the right workflow by classifying the assay and dispatching to the correct nf-core pipeline.
Core Features & Use Cases
- Assay Dispatch: Classifies incoming requests and routes ATAC-seq to nf-core/atacseq, ChIP-seq to nf-core/chipseq, and CUT&RUN/CUT&Tag to nf-core/cutandrun.
- Preflight Validation: Runs a preflight script that checks inputs and emits an install plan before any compute is launched.
- FASTQ Intake and QC: Validates sample sheets, checks read structure, and runs seqkit stats plus FastQC/MultiQC, producing a peak_calling_readiness.json report.
- Use Case: A researcher receives CUT&Tag FASTQ files with IgG controls and needs QC, alignment, and narrow peak calls. The Skill confirms replicates and controls, runs preflight, and hands off to the nf-core/cutandrun workflow.
Quick Start
Ask the assistant to classify your epigenomics assay, verify controls and replicates, and prepare a preflight-first peak-calling plan for your FASTQ files.
