multiqc-stromboli

A MultiQC plugin for the STROMBOLI barcode → variant mapping pipeline.

It reads STROMBOLI's per-sample QC summary files (results/qc/{sample}.stromboli_qc.json) and adds a STROMBOLI section to the MultiQC report: a general-statistics table, a variant-consequence breakdown, a barcode-clash plot, and distribution plots. (cutadapt stats come from MultiQC's built-in cutadapt module.)

Status: working. Wired up against STROMBOLI's summary JSON (workflow/rules/scripts/write_qc_summary.py, schema_version 5): the general-stats table, variant-consequence and variant-type stacked bars (the DMS headline), the ORF coverage profile, the barcode-clash plot, and distribution plots for cluster size, call depth, allele fraction, variants per barcode, barcodes per variant, cluster purity, and barcode length/GC. Counts that span orders of magnitude (cluster size, call depth, variants per barcode, barcodes per variant) are emitted as exact {value: count} and binned by the plugin into data-driven, log-spaced bins shared across the loaded samples, then overlaid one line per sample. Bounded fractions (allele fraction, cluster purity, barcode GC) are pre-binned per-sample histograms (grouped bars, with a Counts / Percentages toggle). See examples/sample.stromboli_qc.json for the shape.

Install

uv tool install multiqc-stromboli      # alongside a MultiQC install, or
uv pip install -e .                     # from a clone, for development

Once installed, MultiQC discovers it automatically via entry points — just run multiqc over a directory containing *stromboli_qc.json files.

Develop

uv sync            # create the venv and install deps (incl. dev)
uv run pytest      # parser unit tests + an end-to-end MultiQC smoke test
                   # (the smoke test self-skips if `multiqc` isn't on PATH)
uv build           # build the wheel/sdist

The QC summary contract

The plugin consumes one JSON file per sample. The expected shape (schema_version 5) is documented by examples/sample.stromboli_qc.json and multiqc_stromboli/parse.py. The producer (STROMBOLI) owns this contract; when the format changes, bump SCHEMA_VERSION in both places. Files with an unexpected schema_version are parsed best-effort with a warning.

License

MIT — see LICENSE.

Getting help

For any issues, please open an issue on the GitHub repository. For questions or feedback, email Chris.