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pacsomatic

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.

plugins/KalarisLabs/research-agent-skills/skills/pacsomatic/SKILL.md

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Nov 6, 2026
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Apache-2.0

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# 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