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
| Parameter | Value | Description |
|---|---|---|
--logger-sumerrs-disable |
warning, error, job_fail; unknown tokens are ignored. Default is error, pass "" to also report errors. |
Comma-separated list of report kinds to disable. |
--logger-sumerrs-out |
&2 (default) is stderr, &1 is stdout, or a file path to append to. |
Where to print the report. |
# 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 byLoggerManager.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
1 maintainer
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