How do I publish a MultiQC report?

`multiqc . -o qc/` writes `qc/multiqc_report.html`, a self-contained interactive page. Publish that file with one curl, or drag it into the app.

Do the interactive plots still work?

Yes. MultiQC's plots are client-side, and report HTML runs scripts inside a sandboxed iframe — hovering a sample, toggling series and switching between plot and table views all behave as they do locally.

Why not email the HTML file?

Because a 40 MB attachment gets bounced or stripped, and an attachment has nowhere for the reply to land. A link opens on a phone, and the note about the outlier sample sits on the plot rather than in a reply chain.

How do I keep one URL per run batch?

PATCH the same report id when you re-run QC for that batch. The collaborator's link keeps working and the earlier version stays as a revision, which matters when someone asks what changed after re-basecalling.

Is the report private?

Private by default, with access set per report — team, email-domain gate, named reviewers, or a password-protected link for an external collaborator. Sample identifiers are frequently more identifying than people expect.

Share a MultiQC report

MultiQC does the aggregation nobody wants to do by hand: forty FastQC outputs, alignment stats, duplication metrics, all collapsed into one interactive page where an outlier sample is visible at a glance.

Then the page is a 30 MB HTML file on a cluster filesystem, and the collaborator who needs it is at another institution with no account on that cluster. So it gets emailed, bounced for size, uploaded to a file service, and discussed in a mail thread where nobody can tell which sample anyone means.

Publish it

multiqc . -o qc/

curl -fsS -X PATCH \
  "https://commareports.com/api/v1/reports/$COMMA_REPORT_ID" \
  -H "Authorization: Bearer $COMMA_API_TOKEN" \
  -H "Content-Type: application/json" \
  -d "$(jq -n --rawfile html qc/multiqc_report.html \
        --arg title "QC — $RUN_ID — $(date +%F)" \
        '{title: $title, html: $html}')"

Or drag multiqc_report.html into the app.

The plots stay interactive at the link — scripts run inside a sandboxed iframe (allow-scripts, no allow-same-origin).

One report id per run batch. PATCH after a re-run keeps the collaborator's link working, with the previous QC still available as a revision — which is the question that comes up after re-basecalling.

What the URL changes

Annotations on the sample. "S14 is the low-input library, expected" pinned to the point on the plot. See commenting on HTML.
Collaborators need no cluster access. A link, in a browser.
Run-over-run comparison. See revisions and diffs.
Private by default. Sample identifiers are often more identifying than they look — see the sharing model, and use a password-protected link for external collaborators.

Limits

HTML body: 5 MB. A MultiQC report over hundreds of samples exceeds this comfortably. Use --flat for static plots, --interactive only where it earns its size, and split by module or by batch — or publish the summary and attach the full report as an asset.
60 requests/minute per token.

Try it

Comma is free — unlimited reports, unlimited commenters, unlimited revision history.

Create your first report →

Nextflow run reports — the pipeline around it
Jupyter notebooks · Quarto
ydata-profiling · Publish from CI

Share a MultiQC report

Publish it

What the URL changes

Limits

Try it

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