# harpy diagnose

Harpy includes a series of diagnose commands to faciliate troubleshooting

The diagnose stall command will run dry-run Snakemake for a workflow with the --dry-run --debug-dag options and print output to try to identify why Snakemake might be stalling for a workflow. This is typically used during development or for troubleshooting edge-cases and you're likely/hopefully not going to need to use this feature. Similar to resume , this requires a Harpy-generated output folder as the sole argument.

harpy diagnose stall path/to/dir

harpy diagnose stall Align/bwa

The diagnose rule command is a shortcut for trying to manually rerun a failing rule.The command will scan the input directory for the most recent Snakemake log file and parse it to identify the first rule triggering the workflow to fail. The input files of the failing rule will be checked for their existence, and if not, Harpy will call Snakemake directly with --no-temp and the missing files as targets to ensure the creation of the missing input files (this is skipped if all input files are present). After, the failing command will be run directly, without invoking Snakemake, in any appropriate container or conda environment.

harpy diagnose rule path/to/dir

harpy diagnose rule Deconvolve/

The output walks you through what Harpy is trying to do: