# USE6.4 Running workflows

## Requirements:

* [[skill-tree:use:5:1:3:b]]
* [[skill-tree:use:4:2:b]]
* optionally: [[skill-tree:sd:3:1:b]]

## Learning Objectivs


* Identify HPC job scheduling systems (e.g. SLURM, LSF, HT-Torque) and describe their role in managing and executing workflows.
* Submit workflows to HPC systems, applying the appropriate Snakemake plugins.
* Utilise job monitoring tools (e.g. squeue/sacct for SLURM) to track the status and performance of running workflows, identify potential issues or bottlenecks.
* Diagnose and troubleshoot common errors:
    * Interpret workflow logs to assess the execution process, identify issues, and validate the correctness of generated results.
    * Report and differentiate between programme failures (due to bugs), workflow or workflow manager issues, and HPC system-level problems (e.g. file system or node failures).
* Collect and manage output data generated during execution, instructing the Workflow Management System to produce publication-ready reports.