Run Snakemake with FlowO

Integrating FlowO into your existing Snakemake execution is as simple as adding a single flag.

The --logger Flag

To enable FlowO reporting, append the --logger flowo argument to your Snakemake command:

snakemake --logger flowo

Customizing the Run

You can provide additional metadata to help organize your runs in the dashboard using logger-specific arguments.

Set a Custom Name

By default, FlowO uses the project directory name. Use --logger-flowo-name to set a more descriptive title.

snakemake --logger flowo --logger-flowo-name "RNA-Seq Sample Analysis"

Add Tags

Use comma-separated tags with --logger-flowo-tags to categorize your runs (e.g., project IDs, sample types, or experimental conditions).

snakemake --logger flowo --logger-flowo-tags "project-x,rna-seq,control"

Associate with a Catalog Entry

If you are running a workflow derived from the FlowO Catalog, specify the slug using --logger-flowo-catalog.

snakemake --logger flowo --logger-flowo-catalog "rna-seq-pipeline"

Configuration via Snakefile/Config

Instead of long command-line arguments, you can define FlowO settings directly in your Snakemake configuration.

In config.yaml:

flowo_project_name: "My Custom Project"
flowo_tags: "experiment-1,debug"

In a Python dict inside the Snakefile:

config["flowo_project_name"] = "My Custom Project"
config["flowo_tags"] = "experiment-1,debug"

Verification

When the logger is active, switch to Runs (/runs) in the browser: the new row should appear within a second or two while jobs stream in over SSE.