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pacsomatic

95 / 100 · Low risk

Fine to try.

By Xircth/VibeX (GitHub) · other · 206 stars · scanned at commit 457d352

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.

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'pacsomatic' ] || [ -L ~/.agents/skills/'pacsomatic' ]; then echo 'A skill folder named pacsomatic already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/Xircth/VibeX' "$d" && git -C "$d" checkout --quiet '457d3525a3554fe9a867feb946c69c830c541fce' -- 'plugins/science/contents/skills/pacsomatic' && mkdir -p ~/.agents/skills && cp -R "$d"/'plugins/science/contents/skills/pacsomatic' ~/.agents/skills/'pacsomatic' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'pacsomatic' ~/.claude/skills/'pacsomatic' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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Score history

Also found in

Identical copies of this skill exist at:

• lilinji/GeneTind-Life-Skills/skills/pacsomatic
• sharkrebel/everything-everywhere-for-antigravity/skills/pacsomatic