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pacsomatic

Validate inputs and generate a samplesheet, params YAML, and launcher script for pacsomatic runs.

22|4|Updated May 25, 2026
Search Tags:#workflow automation#nf-core#nextflow#schedulers#samplesheet#pacsomatic#tumor-normal
One-click install
npx skills add https://github.com/crazymsn/academic-skills --skill pacsomatic-crazymsn
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pacsomatic
Source: https://github.com/crazymsn/academic-skills/tree/main/academic-skills/pacsomatic
Command: npx skills add https://github.com/crazymsn/academic-skills --skill pacsomatic-crazymsn

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This skill provides a reproducible workflow for nf-core/pacsomatic by validating inputs, generating a samplesheet, and creating a launch script that can be run locally or submitted to schedulers.

Core Features & Use Cases

  • Validates required inputs (tumor/normal BAMs, sample and patient IDs, reference selection)
  • Generates a pacsomatic-compliant samplesheet and a Nextflow params YAML for reproducible runs
  • Produces an executable launch script for local or HPC backends (lsf/slurm/pbs/sge) and can submit jobs
  • Helps triage run issues by surfacing validation results and job IDs when available

Quick Start

Provide tumor and normal BAMs, IDs, and a reference, then run the script to generate a samplesheet and a launcher script

Frequently Asked Questions about pacsomatic

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I generate a samplesheet and params YAML for nf-core pacsomatic runs?▼

To generate a pacsomatic samplesheet and params YAML, provide tumor and normal BAMs, sample and patient IDs, and select a reference. The skill validates these inputs and outputs the samplesheet, YAML, and a launch script.

Can I submit pacsomatic Nextflow jobs to an HPC scheduler like Slurm or LSF?▼

Yes, you can submit pacsomatic jobs to HPC schedulers. The generated launch script supports local execution and HPC backends including LSF, Slurm, PBS, and SGE, returning a scheduler job ID if available.

What inputs are required for a tumor-normal pacsomatic workflow?▼

A tumor-normal pacsomatic workflow requires tumor and normal BAM files, sample and patient IDs, and a reference selection. The skill validates these required inputs before generating the samplesheet and launch script.

How do I make Nextflow pacsomatic runs reproducible across different platforms?▼

To make pacsomatic runs reproducible across platforms, the skill generates a compliant samplesheet and a Nextflow params YAML. It validates inputs and creates a launcher script for local or scheduler execution.

Why is my pacsomatic workflow validation failing before job submission?▼

Pacsomatic validation fails when required inputs are missing or invalid. The skill surfaces validation results to help triage run issues, checking tumor and normal BAMs, sample and patient IDs, and reference selection.

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