Update to Life Sciences NGS Analysis

{
  "name": "ngs-chip-cutrun-peaks-qc",
  "description": "Run or plan ChIP-seq, CUT&RUN, or CUT&Tag QC, control handling, spike-in, peak calling, broad-vs-narrow target selection, replicate, bigWig, and differential binding workflows.",
  "included_files": [
    {
      "relative_path": "agents/openai.yaml",
      "size_in_bytes": 292
    }
  ],
  "skill_md_contents": "---\nname: ngs-chip-cutrun-peaks-qc\ndescription: Run or plan ChIP-seq, CUT&RUN, or CUT&Tag QC, control handling, spike-in, peak calling, broad-vs-narrow target selection, replicate, bigWig, and differential binding workflows.\n---\n\n# ChIP/CUT&RUN Peaks QC\n\nUse this skill for antibody-targeted enrichment workflows: ChIP-seq, CUT&RUN, or CUT&Tag. Use `ngs-atacseq-peaks-qc` for ATAC-seq.\n\n## Essential Inputs\n\nConfirm:\n\n- assay: ChIP-seq, CUT&RUN, or CUT&Tag\n- target class: transcription factor, histone mark, chromatin regulator, or custom target\n- FASTQ/BAM inputs and paired-end status\n- input DNA, IgG, no-antibody, or spike-in controls\n- organism, genome build, blacklist, and spike-in genome if used\n- biological replicates, conditions, batches, and sample metadata\n- desired endpoint: QC, peaks, bigWigs, consensus peaks, or differential binding\n\n## Route\n\nUse `nf-core/chipseq` for ChIP-seq and `nf-core/cutandrun` for CUT&RUN/CUT&Tag when they fit the assay. Use direct MACS2 only for prepared BAMs with known control and duplicate policy.\n\nPreflight command:\n\n```bash\npython plugins/ngs-analysis/scripts/ngs_preflight.py --pipeline chip_cutrun_peaks_qc --emit-install-plan\n```\n\nFor compact FASTQ intake/QC, use the shared epigenomics execution package:\n\n```bash\npython plugins/ngs-analysis/scripts/run_fastq_assay_package.py \\\n  --lane epigenomics_peaks \\\n  --sample-sheet chip_or_cutrun_samples.csv \\\n  --execute\n```\n\nIt records FASTQ-level QC and peak-calling readiness.\n\nFor local-light alignment, control-aware MACS2 peak calling, FRiP, bigWig tracks, consensus peaks, and motif-handoff artifacts, use the dedicated ChIP/CUT&RUN runner:\n\n```bash\npython plugins/ngs-analysis/scripts/run_chip_cutrun_peaks_qc.py \\\n  --sample-sheet chip_or_cutrun_samples.csv \\\n  --assay chipseq \\\n  --target-class tf \\\n  --peak-mode narrow \\\n  --bowtie2-index /refs/GRCh38/bowtie2/genome \\\n  --genome-size hs \\\n  --blacklist-bed /refs/GRCh38/blacklists/encode_blacklist.bed \\\n  --execute\n```\n\nThis runner emits `qc/chip_cutrun_qc_summary.{tsv,json}`, `qc/chip_cutrun_qc_dashboard.html`, native SVG FRiP/peak and insert-size plots, browser-track handoff files under `tracks/`, and `motifs/motif_summary.tsv`. Add `--run-motifs --motif-genome <genome>` when HOMER motif enrichment should be executed instead of only planned.\n\nIt also emits `resources/resource_plan.json`, `resource_manifest.tsv`, `resource_env.sh`, and `resource_readiness.md`. The resource check is advisory by default for local-light runs; add `--genome-build`, `--bundle-root <bundle>=<path>`, and `--require-resource-plan` when missing registered reference bundles should block readiness.\n\nFor nf-core execution, use `plugins/ngs-analysis/scripts/run_nfcore_pipeline.py --pipeline chipseq` or `--pipeline cutandrun`.\n\n## Decision Points\n\n- Choose narrow versus broad peak mode from target biology, not from convenience.\n- Preserve control pairing and spike-in metadata through sample sheets.\n- For histone marks, expect broad or domain-like signal for many marks; for TFs, expect sharper peaks and stronger replicate checks.\n- Review alignment rate, duplicate rate, fragment size, FRiP/peak signal, blacklist overlap, and replicate concordance.\n- Keep consensus peak generation and differential binding design separate from raw peak calling.\n\n## Outputs\n\nProduce:\n\n- assay/target/control manifest\n- command/profile and sample sheet\n- QC summary with replicate/control status\n- peaks, bigWigs, browser-track manifests, browser-track preview HTML, native QC dashboard/SVG plots, consensus peaks, and count matrix when requested\n- motif summary files when a motif backend is requested\n- differential binding design and caveats for missing controls, weak enrichment, or poor replicate concordance\n"
}