snakemake-logger-plugin-sumerrs

A Snakemake logger plugin that collects warnings, plain errors and job failures during workflow runs, and reprints them when the run ends. It is a third output channel, in addition to Snakemake's live screen output and its logfile.

Usage

Installation

pip install snakemake-logger-plugin-sumerrs

Enable

Enable the plugin with --logger:

snakemake --logger sumerrs --cores 1

Example

Snakemake ends with 1 failed job and 0 warning

Failed job:
[Sat Aug 22 22:10:34 2026]
Error in rule fail:
    message: None
    jobid: 1
    output: out.txt
    shell:
        false
        (command exited with non-zero exit code)

Settings

# also report errors
snakemake --logger sumerrs --logger-sumerrs-disable ""

# write to stdout (quote it: `&` is a shell metacharacter)
snakemake --logger sumerrs --logger-sumerrs-out '&1'

# append to a file
snakemake --logger sumerrs --logger-sumerrs-out error.log

Behavior

• The plugin stays quiet during the run: it only collects records and prints the report once, when the run ends.
• It is printed directly to the chosen stream and never goes through Snakemake's logging handlers again, so it does not appear in the logfile.
• It is independent of --quiet.
• The report is emitted from close(), i.e. after the logger queue has been drained by LoggerManager.stop().
• Job-failure entries are rendered with Snakemake's DefaultFormatter, so they look exactly like the console output (including --print-logfiles).
• The plugin handler is active only in the main process (ExecMode.DEFAULT); subprocess/remote job processes skip plugin handlers.

Development

pixi install
pixi run test
# or
pixi run -e test pytest