pacsomatic

Overview

This skill provides a reproducible execution workflow for nf-core/pacsomatic, centered on a single helper entrypoint that handles validation, artifact generation, and optional execution.

Primary entrypoint:

• scripts/run_pacsomatic.py

The helper script:

• 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

Use this skill as the default path for pacsomatic operations. Do not bypass it with manually assembled nextflow run nf-core/pacsomatic commands unless the user explicitly asks for manual command construction.

When to Use This Skill