pacsomatic

SUMMARY

What it does

This skill provides a reproducible execution workflow for nf-core/pacsomatic, centered on a single helper entrypoint (scripts/run_pacsomatic.py) that handles validation, artifact generation, and optional execution. It validates required identifiers, files, reference mode, and runtime prerequisites; writes a pacsomatic-compatible samplesheet (patient,sample,status,bam,pbi); generates a params YAML and launch script for reproducible reruns; supports dry-run validation and run/submit execution paths. It is intended for running matched tumor-normal analysis from BAM files, generating or fixing samplesheets and launch artifacts, executing locally or submitting to schedulers (LSF/Slurm/PBS/SGE), performing dry-run validation, and troubleshooting launch failures. It is not intended for deep biological interpretation or editing pipeline internals unless explicitly requested.