ema wizard (and bare ema)

An interactive questionary-based wizard that walks you through assembling a config for any of PeakATail's main commands, saves it to .peakatail/last_run.yaml, and dispatches into the same code path as the explicit CLI invocations.

ema with no subcommand also drops you into this wizard — handy for first-time users who haven't memorised the flag set yet.

When to use it

• First exposure to PeakATail — you don't know the flag names yet.
• Quickly assembling a config to save and re-use as --config last_run.yaml.
• Teaching workshops — the prompts double as a discoverable parameter inventory.

When NOT to use it

• Scripted / unattended runs (CI, Docker, batch jobs) — questionary requires a TTY. Use the explicit subcommands with --config instead.

Quick example

# Bare ema also routes here
uv run ema

# Or explicitly
uv run ema wizard

The wizard first asks which mode you want:

? What do you want to do?
  > Run full pipeline (peak calling -> cluster)
    Differential APA test (ema switch diff)
    3'UTR shortening / lengthening (ema switch length)
    Cross-dataset cluster matching (ema switch match)
    Merge BAMs (ema merge)
    Pre-warm GTF cache (ema parse-gtf)

Then sequences mode-specific prompts (paths to BAMs, GTF, strategy, FDR, output dir, etc.) and finally asks:

? Save this config to .peakatail/last_run.yaml? (Y/n)
? Proceed to run now? (Y/n)

If you decline the run, the YAML is still on disk so you can launch it later via:

uv run ema run --config .peakatail/last_run.yaml

Full --help output

Usage: ema wizard [OPTIONS]

  Launch the interactive wizard explicitly.

Options:
  -h, --help  Show this message and exit.

No flags — the wizard takes everything via prompts.

Modes dispatched

Wizard option	Dispatches to
Run full pipeline	ema run
Differential APA test	ema switch diff
3'UTR shortening/lengthening	ema switch length
Cross-dataset cluster matching	ema switch match
Merge BAMs	ema merge
Pre-warm GTF cache	ema parse-gtf

Output files

.peakatail/last_run.yaml — the configuration you assembled (only written if you answer "yes" to the save prompt). Re-usable via any of the matching subcommands' --config flag.

After dispatch, the chosen subcommand writes its own outputs to peakatail_runs/<name>_<ts>/ (see each subcommand's page).

See also

• All the subcommands the wizard dispatches into — linked in the table above.
• Quickstart tutorial — covers the same ground in static command form.