Function write_visuals

plugins/ngs-analysis/scripts/run_nfcore_pipeline.py:267–372

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

def write_visuals(
    run_dir: Path,
    status: str,
    validation: dict[str, Any],
    resource_plan: dict[str, Any] | None,
) -> dict[str, str]:
    entries = [
        artifact_entry(
            artifact_id="params",
            title="Generated Params",
            path="workflow/params.generated.json",
            kind="json",
            status="created",
            description="Nextflow params generated by the plugin adapter.",
        ),
        artifact_entry(
            artifact_id="command",
            title="Nextflow Command",
            path="workflow/nfcore_command.json",
            kind="json",
            status="created",
            description="Exact command used or ready to run.",
        ),
        artifact_entry(
            artifact_id="nextflow_report",
            title="Nextflow Report",
            path="workflow/nextflow_report.html",
            kind="html",
            status="created"
            if (run_dir / "workflow" / "nextflow_report.html").exists()
            else "not_available",
            description="Nextflow execution report, emitted after a successful or partially successful run.",
        ),
    ]
    if resource_plan is not None:
        entries.extend(
            [
                artifact_entry(
                    artifact_id="resource_readiness",
                    title="Resource Readiness",
                    path="resources/resource_readiness.md",
                    kind="markdown",
                    status="created",
                    description="Human-readable reference/database readiness gate for this nf-core run.",
                ),
                artifact_entry(
                    artifact_id="resource_manifest",
                    title="Resource Manifest",
                    path="resources/resource_manifest.tsv",
                    kind="table",
                    status="created",
                    description="Pipeline resource bundles, roots, env vars, and missing-file counts.",
                ),
                artifact_entry(
                    artifact_id="resource_plan",
                    title="Resource Plan",
                    path="resources/resource_plan.json",
                    kind="json",