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pacsomatic

by Scientific Skills

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.

v1.0.0New
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Install this skill

Run this command in your terminal. No account required — it auto-detects your AI tool and installs the skill file.

npx @skills-hub-ai/cli install scientific-skills-pacsomatic
Or download directly:
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Setup by platform

Claude Code

~/.claude/skills/<skill>/SKILL.md

Setup guide →

Install

One-click setup for your editor

Run in your project root

npx @skills-hub-ai/cli install scientific-skills-pacsomatic --target claude-code

Instructions

This skill doesn’t include stateful context yet, instructions only. Learn about stateful skills.

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Frequently asked questions about pacsomatic

What does the pacsomatic skill do?

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. It's a reusable SKILL.md instruction set that loads into your AI coding assistant on demand, no prompt engineering, no copy-pasting every session.

How do I install the pacsomatic skill?

Run `npx @skills-hub-ai/cli install scientific-skills-pacsomatic` from your terminal. The CLI writes the SKILL.md to the correct location for your AI tool (e.g. ~/.claude/skills/scientific-skills-pacsomatic/ for Claude Code or ~/.cursor/skills/ for Cursor with --target cursor) and adds it to your project's .skills.json lockfile.

Which AI tools does pacsomatic work with?

pacsomatic runs in Claude Code. It follows the open Agent Skills standard (SKILL.md), so the same skill works in every supported tool without modification.

Is the pacsomatic skill free?

Yes. Every skill on skills-hub.ai is free and open-source. There are no premium tiers, paywalls, or usage limits. You only pay for whatever AI assistant you're already using.

How do I use pacsomatic after installing it?

In Claude Code, type `/scientific-skills-pacsomatic` (or whatever slash command the skill registers) and the AI follows the skill's instructions immediately. You can also reference it by name in natural language, your AI loads the skill into context when relevant.

Can I share the pacsomatic skill with my team?

Yes. Commit your project's .skills.json lockfile and teammates run `npx @skills-hub-ai/cli install` (no args) to install every skill at the exact version you pinned. Organization-scoped installs work via skills-hub.ai organizations.