Snakemake logger plugin: biffix

Warning

This plugin is not maintained and reviewed by the official Snakemake organization.

Warning

No documentation found in repository https://github.com/nh13/biffix. The plugin should provide a docs/intro.md with some introductory sentences and optionally a docs/further.md file with details beyond the auto-generated usage instructions presented in this catalog.

Installation

Install this plugin by installing it with pip or mamba directly, e.g.:

pip install snakemake-logger-plugin-biffix

Or, if you are using pixi, add the plugin to your pixi.toml. Be careful to put it under the right dependency type based on the plugin’s availability, e.g.:

snakemake-logger-plugin-biffix = "*"

Usage

In order to use the plugin, run Snakemake (>=9.11) with the corresponding value for the logger flag:

snakemake --logger biffix ...

with ... being any additional arguments you want to use.

Settings

The logger plugin has the following settings (which can be passed via command line, the workflow or environment variables, if provided in the respective columns):

Settings

CLI argument	Description	Default	Choices	Required	Type
--logger-biffix-run-id VALUE	biffix run id this workflow belongs to.	''		✗
--logger-biffix-ingest-url VALUE	biffix ingest route base URL.	''		✗
--logger-biffix-ingest-token VALUE	Per-run capability token (a secret; prefer the BIFFIX_INGEST_TOKEN env var).	''		✗
--logger-biffix-event-file VALUE	Name of the durable events.jsonl archival replay copy, relative to the directory Snakemake starts in (default: BIFFIX_EVENT_FILE, else .biffix_events.jsonl).	''		✗