nf-diff

My pipeline behaved differently this time — what actually changed?

nf-diff is a Nextflow plugin that adds a diff CLI verb. Point it at two runs from your local run history — or just say --last — and it reconstructs both entirely from Nextflow’s own history and cache (no re-execution) and renders a self-contained HTML report of everything that changed between them.

nextflow plugin nf-diff:diff --last

What it compares

Metadata & parameters

Were the runs launched differently? Flag-by-flag diff of launch options and -params-file values, tagged by source.

Configuration

Did the resolved nextflow.config change once profiles are applied?

Processes & tasks

Which processes gained or lost tasks, and how did each task’s status, exit code, script, and resource usage change?

Software & versions

Did a container image or Conda pin change?

Failures

What failed, and is it new, resolved, or persistent across the two runs?

Performance & efficiency

Did any task get slower or heavier, or was it over- or under-provisioned?

Outputs & published results

Did the files each task produced actually change, line by line?

Logs & DAG

Why did a task’s exit code change, and was the pipeline rewired?

By default the report highlights meaningful changes and treats always-differing fields (run name, session id, launch time, cache hash, wall time, resource usage) as context. Use --verbose to flag everything. See Comparison layers for what each layer detects.

Output

A single, standalone HTML document — inline CSS/JS/SVG, no network access, light/dark theme — that you can open in a browser or email to a colleague. It’s paginated behind a vertical sidebar, and the performance page leads with a diverging-bar chart of the biggest movers. For CI and scripting, --format=json and --format=md emit the same comparison, and --fail-on-change turns any difference into a non-zero exit code.

See it in action in the Gallery.

Quick start

# Compare the two most recent runs
nextflow plugin nf-diff:diff --last

# Compare two runs by name (or session-id prefix)
nextflow plugin nf-diff:diff tender_euler happy_curie

# Emit Markdown for a PR comment
nextflow plugin nf-diff:diff --last --format=md --output=diff.md

# CI gate: fail if anything meaningful changed
nextflow plugin nf-diff:diff --last --fail-on-change

Continue with the full Usage reference for installation and every option.