run-cso

To run the Cancer Signal Origin (CSO) pipeline for clinical genomics samples, you provide a clinical report file and specify an output directory. The skill then manages automated pipeline execution and SLURM job scheduling.

Yes, you can analyze archived clinical samples using the CSO caller pipeline. The skill performs intelligent pre-checks for archived samples and handles automatic retrieval to streamline the genomics analysis workflow.

SLURM job management for genomic pipeline execution is fully automated by the skill. It handles prerequisite validation, submits the pipeline jobs, monitors progress in real-time, and gracefully manages any execution timeouts.

To customize the CSO caller pipeline, you can configure BIP settings, execution timeouts, and project naming conventions. These custom configurations help streamline and tailor the genomic data analysis workflow to your specific needs.

To monitor progress during cancer signal origin analysis, the skill provides real-time updates and handles timeouts gracefully. This ensures automated SLURM pipeline execution runs reliably without manual intervention for stalled jobs.

Prerequisite validation is necessary before running the CSO pipeline to ensure the clinical sample analysis environment is correctly configured. The skill automates these pre-checks to prevent execution errors and streamline genomics workflows.