pacsomatic

97 / 100 · Low risk

Fine to try.

By K-Dense-AI/claude-scientific-skills (GitHub) · data · 57,146 stars · scanned at commit 2d2065f

Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs. Supports samplesheet generation, pinned Nextflow launch artifacts, local checks, LSF/Slurm/PBS Pro/SGE launcher submission, and startup troubleshooting. Use for pacsomatic run preparation and execution, not general short-read somatic analysis or medical imaging PACS.

Works with any agent that supports SKILL.md skills.

What this skill can do

Runs commands on your computer

This is disclosed by the author in the skill's SKILL.md or README.

Found in 12 places.

skills/pacsomatic/SKILL.md, line 73python skills/pacsomatic/scripts/run_pacsomatic.py \
skills/pacsomatic/SKILL.md, line 103uv run skills-ref validate skills/pacsomatic
skills/pacsomatic/scripts/run_pacsomatic.py, line 76completed = subprocess.run([java, "-version"], capture_output=True, text=True, timeout=30)

Show 9 more

skills/pacsomatic/scripts/run_pacsomatic.py, line 122completed = subprocess.run(cmd)
skills/pacsomatic/scripts/run_pacsomatic.py, line 126completed = subprocess.run(["git", "-C", str(target), "checkout", "--detach", args.pipeline_version])
skills/pacsomatic/scripts/run_pacsomatic.py, line 130result = subprocess.run(["git", "-C", str(target), "rev-parse", "HEAD", args.pipeline_version], capture_output=True, text=True)
skills/pacsomatic/scripts/run_pacsomatic.py, line 166completed = subprocess.run(cmd, capture_output=True, text=True)
skills/pacsomatic/scripts/run_pacsomatic.py, line 188completed = subprocess.run(cmd)
skills/pacsomatic/scripts/run_pacsomatic.py, line 562result = subprocess.run([args.nextflow_bin, "-version"], capture_output=True, text=True, timeout=60)
skills/pacsomatic/scripts/run_pacsomatic.py, line 693completed = subprocess.run(argv)
skills/pacsomatic/scripts/run_pacsomatic.py, line 700completed = subprocess.run(argv, stdin=handle, text=True, capture_output=True)
skills/pacsomatic/scripts/run_pacsomatic.py, line 702completed = subprocess.run(argv, text=True, capture_output=True)

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=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/K-Dense-AI/claude-scientific-skills' "$d" && git -C "$d" checkout --quiet '2d2065fb4520fa3f3f2bcf61cff26ec8b7eba4b5' -- 'skills/pacsomatic' && mkdir -p ~/.agents/skills && cp -R "$d"/'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

Date	Version	Score
2026-11-10	`2d2065f`	97
2026-11-08	`a25cf9e`	97
2026-11-07	`a25cf9e`	97

Also found in

Identical copies of this skill exist at:

K-Dense-AI/scientific-agent-skills/skills/pacsomatic