(
run_dir: Path,
status: str,
validation: dict[str, Any],
resource_plan: dict[str, Any] | None = None,
)
| 837 | |
| 838 | |
| 839 | def write_visuals( |
| 840 | run_dir: Path, |
| 841 | status: str, |
| 842 | validation: dict[str, Any], |
| 843 | resource_plan: dict[str, Any] | None = None, |
| 844 | ) -> dict[str, str]: |
| 845 | entries = [ |
| 846 | artifact_entry( |
| 847 | artifact_id="samples", |
| 848 | title="Amplicon Samples", |
| 849 | path="validation/samples.normalized.tsv", |
| 850 | kind="table", |
| 851 | status="created", |
| 852 | description="Normalized sample FASTQ manifest.", |
| 853 | ), |
| 854 | artifact_entry( |
| 855 | artifact_id="command_plan", |
| 856 | title="Backend Command Plan", |
| 857 | path="workflow/amplicon_backend_command_plan.json", |
| 858 | kind="json", |
| 859 | status="created", |
| 860 | description="QIIME2, DADA2, or nf-core/ampliseq command contract.", |
| 861 | ), |
| 862 | artifact_entry( |
| 863 | artifact_id="methods", |
| 864 | title="Backend Methods", |
| 865 | path="methods/amplicon_backend_methods.json", |
| 866 | kind="json", |
| 867 | status="created", |
| 868 | description="Primer, marker, taxonomy, and diversity method contract.", |
| 869 | ), |
| 870 | artifact_entry( |
| 871 | artifact_id="backend_summary", |
| 872 | title="Backend Export Summary", |
| 873 | path="tables/amplicon_backend_summary.json", |
| 874 | kind="json", |
| 875 | status="created", |
| 876 | description="Records which QIIME2/DADA2/nf-core exported tables were normalized for review.", |
| 877 | ), |
| 878 | artifact_entry( |
| 879 | artifact_id="diversity_summary", |
| 880 | title="Diversity Summary", |
| 881 | path="tables/amplicon_diversity_summary.json", |
| 882 | kind="json", |
| 883 | status="created", |
| 884 | description="Backend-derived alpha diversity, Bray-Curtis, and taxa-plot availability summary.", |
| 885 | ), |
| 886 | artifact_entry( |
| 887 | artifact_id="backend_dashboard", |
| 888 | title="Backend Dashboard", |
| 889 | path="visualizations/amplicon_backend_dashboard.html", |
| 890 | kind="html", |
| 891 | status="created", |
| 892 | description="Native review dashboard for ASV depth, alpha diversity, taxa/features, and backend caveats.", |
| 893 | ), |
| 894 | artifact_entry( |
| 895 | artifact_id="sample_depth_plot", |
| 896 | title="Sample Depth Plot", |
no test coverage detected