Update to Life Sciences NGS Analysis

{
  "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.",
  "included_files": [
    {
      "relative_path": "agents/openai.yaml",
      "size_in_bytes": 277
    }
  ],
  "skill_md_contents": "---\nname: ngs-epigenomics-peaks\ndescription: 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.\n---\n\n# Epigenomics Peaks\n\nUse 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.\n\n## Essential Inputs\n\nConfirm:\n\n- assay type\n- FASTQ or BAM input\n- organism and genome build\n- blacklist file, if available\n- control samples: input DNA, IgG, or spike-in\n- biological replicates\n- peak type: narrow, broad, accessibility, or protocol-specific\n- desired outputs: QC report, peaks, consensus peaks, bigWigs, differential peaks\n\n## Public Defaults\n\nChoose the workflow by assay:\n\n- ATAC-seq: `ngs-atacseq-peaks-qc` using `nf-core/atacseq` by default\n- ChIP-seq: `ngs-chip-cutrun-peaks-qc` using `nf-core/chipseq` by default\n- CUT&RUN or CUT&Tag: `ngs-chip-cutrun-peaks-qc` using `nf-core/cutandrun` by default\n\nUse direct MACS2 only for focused peak-calling tasks from prepared BAMs.\n\n## Preflight\n\n```bash\npython plugins/ngs-analysis/scripts/ngs_preflight.py --pipeline epigenomics_peaks --emit-install-plan\n```\n\n## Local Execution Package\n\nFor FASTQ intake/QC over ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag data, use the shared FASTQ assay package:\n\n```bash\npython plugins/ngs-analysis/scripts/run_fastq_assay_package.py \\\n  --lane epigenomics_peaks \\\n  --sample-sheet assay_samples.csv \\\n  --execute\n```\n\nThis 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.\n\nAssay-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.\n\n## Kickoff Pattern\n\nATAC-seq preflight run:\n\n```bash\nnextflow run nf-core/atacseq \\\n  -profile test,docker \\\n  --outdir results/atacseq_test\n```\n\nChIP-seq preflight run:\n\n```bash\nnextflow run nf-core/chipseq \\\n  -profile test,docker \\\n  --outdir results/chipseq_test\n```\n\nCUT&RUN/CUT&Tag preflight run:\n\n```bash\nnextflow run nf-core/cutandrun \\\n  -profile test,docker \\\n  --outdir results/cutandrun_test\n```\n\nCarry replicate and control metadata through the sample sheet before running real analysis.\n"
}