pacsomatic (Claude Skill)

Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs.

   
Type Claude Skill
Supplier K-Dense Inc. (community OSS)
Availability GA — part of the actively maintained K-Dense scientific-agent-skills collection
Pricing Free / OSS (MIT)
Capabilities Read/Write — Claude runs the skill’s Python locally (Bash), not as an MCP tool

How to install

  • Claude Code / Claude.ai — Skills CLI (recommended): 
    npx skills add K-Dense-AI/scientific-agent-skills

    Installs the K-Dense collection; enable the pacsomatic skill when prompted. Works across Claude Code, Cursor, and Codex via the Agent Skills spec (requires Node ≥ 18).

  • Claude Code / Claude Desktop — manual clone: 
    git clone https://github.com/K-Dense-AI/scientific-agent-skills
cp -r scientific-agent-skills/skills/pacsomatic ~/.claude/skills/

    Project-scoped alternative: copy into .claude/skills/ instead of ~/.claude/skills/. The skill declares its own Python dependencies in its SKILL.md; install them (the K-Dense skills generally use uv / pip) when prompted on first use.

What it does

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.

Primary use cases: 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.

Notes

Distributed as a SKILL.md (plus code examples) in the K-Dense collection — Claude executes it locally via Bash/Python rather than as an MCP server. Upstream license: MIT. The skill name to enable after install is pacsomatic.

Sources

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