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

Invoke this skill when the user asks to:

• run matched tumor-normal analysis from BAM files
• generate or fix pacsomatic samplesheet and launch artifacts
• execute locally or submit to schedulers (LSF/Slurm/PBS/SGE)
• perform dry-run validation before execution
• troubleshoot launch failures or summarize run outputs

Do not use this skill for:

• deep biological interpretation beyond run-level sanity checks
• editing pipeline internals unless explicitly requested

Typical trigger phrases:

• "run nf-core/pacsomatic for this tumor-normal pair"
• "prepare pacsomatic samplesheet and launch script"
• "do a dry run first and tell me what is missing"
• "submit pacsomatic to slurm/lsf and return the job id"
• "why did pacsomatic submission fail"

Routing and Execution Rules

1. Always collect required run inputs first.