ngs-epigenomics-peaks
GitHub作为表观遗传学分析的分发器，处理ATAC-seq、ChIP-seq等数据的质控、比对及峰调用。根据实验类型自动路由至对应工作流，支持本地执行包与预检，并生成QC报告及可视化文件。
Trigger Scenarios
Install
npx skills add openai/plugins --skill ngs-epigenomics-peaks -g -y
SKILL.md
Frontmatter
{
"name": "ngs-epigenomics-peaks",
"description": "Dispatch ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag requests to assay-specific QC, alignment, signal-track, peak-calling, consensus, and differential peak workflows."
}
Epigenomics Peaks
Use this skill as the epigenomics dispatcher for ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag analysis. Hand off to the assay-specific deep skill once the assay type is known.
Essential Inputs
Confirm:
- assay type
- FASTQ or BAM input
- organism and genome build
- blacklist file, if available
- control samples: input DNA, IgG, or spike-in
- biological replicates
- peak type: narrow, broad, accessibility, or protocol-specific
- desired outputs: QC report, peaks, consensus peaks, bigWigs, differential peaks
Public Defaults
Choose the workflow by assay:
- ATAC-seq:
ngs-atacseq-peaks-qcusingnf-core/atacseqby default - ChIP-seq:
ngs-chip-cutrun-peaks-qcusingnf-core/chipseqby default - CUT&RUN or CUT&Tag:
ngs-chip-cutrun-peaks-qcusingnf-core/cutandrunby default
Use direct MACS2 only for focused peak-calling tasks from prepared BAMs.
Preflight
python plugins/ngs-analysis/scripts/ngs_preflight.py --pipeline epigenomics_peaks --emit-install-plan
Local Execution Package
For FASTQ intake/QC over ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag data, use the shared FASTQ assay package:
python plugins/ngs-analysis/scripts/run_fastq_assay_package.py \
--lane epigenomics_peaks \
--sample-sheet assay_samples.csv \
--execute
This validates sample-sheet paths and read structure, runs seqkit stats and FastQC/MultiQC when available, and writes peak_calling_readiness.json. Full alignment, signal tracks, TSS/FRiP, consensus peaks, and differential analyses still route through the assay-specific workflow.
Assay-specific ATAC and ChIP/CUT&RUN runners now also emit native review files alongside TSV/JSON summaries: qc/*_dashboard.html, FRiP/peak SVG plots, insert-size SVG plots, browser-track preview HTML, UCSC track lines, and IGV session files.
Kickoff Pattern
ATAC-seq preflight run:
nextflow run nf-core/atacseq \
-profile test,docker \
--outdir results/atacseq_test
ChIP-seq preflight run:
nextflow run nf-core/chipseq \
-profile test,docker \
--outdir results/chipseq_test
CUT&RUN/CUT&Tag preflight run:
nextflow run nf-core/cutandrun \
-profile test,docker \
--outdir results/cutandrun_test
Carry replicate and control metadata through the sample sheet before running real analysis.
Version History
- 11c74d6 Current 2026-07-19 09:42
