Pacsomatic

---
name: pacsomatic
description: Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user needs to validate run inputs, generate pacsomatic-compliant samplesheets, prepare reproducible Nextflow launch artifacts, run locally or submit to schedulers (LSF/Slurm/PBS/SGE), and triage execution failures. Triggers on requests to run pacsomatic, prepare launch commands/scripts, perform dry-run checks, or troubleshoot pipeline startup and scheduler submission errors.
license: MIT
metadata: {"version": "1.0", "skill-author": "Beifang Niu", "contributors": "Haidong, Wenchao", "upstream-pipeline": "https://github.com/nf-core/pacsomatic"}
---

# 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… load the full skill through Skill Me