Function write_visuals

plugins/ngs-analysis/scripts/run_atacseq_peaks_qc.py:389–507

(
    run_dir: Path,
    status: str,
    validation: dict[str, Any],
    resource_plan: dict[str, Any] | None = None,
)

def write_visuals(
    run_dir: Path,
    status: str,
    validation: dict[str, Any],
    resource_plan: dict[str, Any] | None = None,
) -> dict[str, str]:
    entries = [
        artifact_entry(
            artifact_id="samples",
            title="ATAC Samples",
            path="validation/samples.normalized.tsv",
            kind="table",
            status="created",
            description="Normalized ATAC sample table.",
        ),
        artifact_entry(
            artifact_id="command_plan",
            title="ATAC Command Plan",
            path="workflow/atacseq_command_plan.json",
            kind="json",
            status="created",
            description="Alignment, filtering, peak, FRiP, signal, and TSS command plan.",
        ),
        artifact_entry(
            artifact_id="qc_contract",
            title="ATAC QC Contract",
            path="qc/atac_qc_contract.json",
            kind="json",
            status="created",
            description="Metrics required for interpretation and artifacts expected after execution.",
        ),
        artifact_entry(
            artifact_id="qc_summary",
            title="ATAC QC Summary",
            path="qc/atacseq_qc_summary.tsv",
            kind="table",
            status="created",
            description="Parsed per-sample alignment, insert-size, FRiP, peak, TSS, motif, and track state.",
        ),
        artifact_entry(
            artifact_id="qc_dashboard",
            title="ATAC QC Dashboard",
            path="qc/atacseq_qc_dashboard.html",
            kind="html",
            status="created",
            description="Native dashboard summarizing FRiP, peak counts, insert sizes, track state, and caveats.",
        ),
        artifact_entry(
            artifact_id="frip_peak_overview",
            title="FRiP And Peak Plot",
            path="qc/atacseq_qc_frip_peak_overview.svg",
            kind="svg",
            status="created",
            description="Compact FRiP and peak-count plot generated from parsed run artifacts.",
        ),
        artifact_entry(
            artifact_id="insert_size_distribution",
            title="Insert-Size Plot",