Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add crazymsn/academic-skills --skill pacsomaticgit clone --depth 1 https://github.com/crazymsn/academic-skillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/crazymsn/academic-skills/pacsomatic)<a href="https://agentmods.dev/skills/crazymsn/academic-skills/pacsomatic"><img src="https://agentmods.dev/badge/skills/crazymsn/academic-skills/pacsomatic/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/crazymsn/academic-skills/pacsomatic"><img src="https://agentmods.dev/badge/skills/crazymsn/academic-skills/pacsomatic.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00103 | $0.01201 |
| Opus 5 | $0.00051 | $0.00600 |
| Sonnet 5 | $0.00021 | $0.00240 |
| Haiku 4.5 | $0.00010 | $0.00120 |
Grade A, and why
pacsomatic scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 8d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
This is a copy
100% identical to pacsomatic — 3 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 150 lines — stays where its author put it; the contents beside it link to each section on GitHub.
pacsomatic
Overview
This skill provides a reproducible execution workflow for nf-core/pacsomatic, centered on a single helper entrypoint that handles validation, artifact generation, and optional execution.
Primary entrypoint:
scripts/run_pacsomatic.py
The helper script:
- validates required identifiers, files, reference mode, and runtime prerequisites
- writes a pacsomatic-compatible samplesheet (
patient,sample,status,bam,pbi) - generates a params YAML and launch script for reproducible reruns
- supports dry-run validation and run/submit execution paths
Use this skill as the default path for pacsomatic operations. Do not bypass it with manually assembled nextflow run nf-core/pacsomatic commands unless the user explicitly asks for manual command construction.
When to Use This Skill
Invoke this skill when the user asks to:
- run matched tumor-normal analysis from BAM files
- generate or fix pacsomatic samplesheet and launch artifacts
- execute locally or submit to schedulers (LSF/Slurm/PBS/SGE)
- perform dry-run validation before execution
- troubleshoot launch failures or summarize run outputs
Do not use this skill for:
- deep biological interpretation beyond run-level sanity checks
- editing pipeline internals unless explicitly requested
Typical trigger phrases:
- "run nf-core/pacsomatic for this tumor-normal pair"
- "prepare pacsomatic samplesheet and launch script"
- "do a dry run first and tell me what is missing"
- "submit pacsomatic to slurm/lsf and return the job id"
- "why did pacsomatic submission fail"
Routing and Execution Rules
- Always collect required run inputs first.
- Always route through
scripts/run_pacsomatic.pyfor validation and artifact generation. - Default to
--dry-runwhen the user asks for checks/validation only. - Use
--runonly when the user asks to execute/submit. - For scheduler modes, include executor-specific resource arguments and return detected job ID when available.
- If execution fails, report first failure point and next triage target (
.nextflow.log,pipeline_info, failing task logs).
What ships with it
7 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 8d ago First seen · 150 lines · 103 tokens per session scan A 178da103b16d
pacsomatic is a skill published in the GitHub repository crazymsn/academic-skills (22 stars, last pushed 3mo ago), licensed MIT. It adds 103 tokens to every session and 1,201 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 0 findings. It is 100% identical to pacsomatic, differing in 3 lines, and is treated as a copy.
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