Pacsomatic Skill

Agent-oriented skill assets for operating the nf-core/pacsomatic matched tumor-normal pipeline.

This repository provides a runnable helper script and agent guidance documents. Start with this README for execution basics. Use SKILL.md for the full agent execution contract.

Minimal Inputs

Required run inputs:

• tumor BAM path
• normal BAM path
• output directory
• one reference mode: --fasta or --genome

Quick Start

Dry-run validation command:

python scripts/run_pacsomatic.py \
  --tumor-bam /path/to/tumor.bam \
  --normal-bam /path/to/normal.bam \
  --patient-id P001 \
  --tumor-sample-id P001_T \
  --normal-sample-id P001_N \
  --outdir /path/to/output \
  --genome GRCh38 \
  --profile singularity,sanger \
  --dry-run

Run mode command (local example):

python scripts/run_pacsomatic.py \
  --tumor-bam /path/to/tumor.bam \
  --normal-bam /path/to/normal.bam \
  --patient-id P001 \
  --tumor-sample-id P001_T \
  --normal-sample-id P001_N \
  --outdir /path/to/output \
  --fasta /path/to/reference.fa \
  --profile singularity,sanger \
  --executor local \
  --run

Repository Layout

• SKILL.md: agent operating protocol and troubleshooting logic
• scripts/run_pacsomatic.py: helper entrypoint
• environment/nextflow-env.yml: environment template
• references/agent-playbook.md: concise operation playbook
• references/config-and-output.md: config/output mapping
• references/pacsomatic_guide.md: extended usage notes

Notes

• Run dry-run first in new environments.
• Scheduler execution is selected with --executor (lsf, slurm, pbs, sge).
• Full behavior contract, triage order, and response requirements are defined in SKILL.md.