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CD single-cell-preprocessing-with-omicverse

Walk through omicverse's single-cell preprocessing tutorials to QC PBMC3k data, normalise counts, detect HVGs, and run PCA/embedding pipelines on CPU, CPU–GPU mixed, or GPU stacks.

FreedomIntelligence/OpenClaw-Medical-Skills Agent Skills author: FreedomIntelligence 2 files body ≈ 2 766 tokens Open the sourcegithub.com↗ analyzed 14 h ago

Walk through omicverse's single-cell preprocessing tutorials to QC PBMC3k data, normalise counts, detect HVGs, and run PCA/embedding pipelines on CPU, CPU–GPU…

As a process D 47/100 · Unfinished process — References files that are not bundled: ../../omicverse_guide/docs/Tutorials-single/t_preprocess.ipynb, ../../omicverse_guide/docs/Tutorials-single/t_preprocess_cpu.ipynb, ../../omicverse_guide/docs/Tutorials-single/t_preprocess_gpu.ipynb

ProcedureData and analyticsInfrastructureAI and agentstype and topics are labelled automatically from the skill text
Runs in: Claude / Claude Code ChatGPT / Codex Gemini CLI Cursor GitHub Copilot / VS Code Qwen Code Kimi Code CLI Z.ai (GLM) DeepSeek (Deep Code) Mistral Vibe LangChain (deepagents) OpenClaw Goose OpenCode
JSON
Technical rating
C
81/100
safety, quality, tests
Safety 60%
95
Quality 40%
59
Run on models
none yet
Process rating
D
47/100
Unfinished process
References files that are not bundled: ../../omicverse_guide/docs/Tutorials-single/t_preprocess.ipynb, ../../omicverse_guide/docs/Tutorials-single/t_preprocess_cpu.ipynb, ../../omicverse_guide/docs/Tutorials-single/t_preprocess_gpu.ipynb
Tools and files w 18
0
Result and completion w 14
0
Consistency w 8
40
the three weakest of ten parameters · all ten

What is at stake

Medium-severity findings: the skill is probably honest, but read what alarmed the scanner.

Dangerous commands medium severity

Below is the worst case for this category. The finding here is medium: the guard saw a sign, not a proof.

If you install

The skill contains commands that delete files, rewrite disks or execute code fetched from the network. The agent may run them without asking if it believes the instructions require it.

For the author

Replace destructive commands with safe equivalents that ask for confirmation, scope them to one folder, and stop piping curl into a shell: pin a version and a checksum.

How to improve

  1. Say in the description WHEN to use the skill ("use when…", example requests): that is the agent's main cue.
  2. The text references files that are not there: add them or drop the references.
For the model run — optional
  • Your own cases (evals/evals.json, 4–6 real requests with expected answers): the full check would then run those instead of a model-drafted suite.
  • A spec.yaml with trigger phrases and assertions — a behaviour contract for CI; `skilltest init` writes a template.

Guard findings · 1

✓ No critical or high findings

Medium and low: 1
  • medium Dangerous commands cmd-pipe-to-shell-known-host reference.md:19
    Pipe-to-shell installer from a well-known host (still executes remote code)
    curl -sSL https://raw.githubusercontent.com/Starlitnightly/omicverse/refs/heads/master/install.sh | bash -s

Files scanned: 2. Evidence is masked. Grey chips explain why severity was lowered.

Against the Agent Skills spec

  • warning description-no-when description does not say WHEN to use the skill (no "use when")
  • warning missing-ref reference to a missing file: ../../omicverse_guide/docs/Tutorials-single/t_preprocess.ipynb
  • warning missing-ref reference to a missing file: ../../omicverse_guide/docs/Tutorials-single/t_preprocess_cpu.ipynb
  • warning missing-ref reference to a missing file: ../../omicverse_guide/docs/Tutorials-single/t_preprocess_gpu.ipynb
  • note frontmatter-key unknown frontmatter key "title"
  • note edit-residue the text marks something as outdated (lines 9): check that old rules are not kept next to new ones — the full check reads the text for contradictions

Process rating: all ten parameters 47/100

Will not run. References files that are not bundled: ../../omicverse_guide/docs/Tutorials-single/t_preprocess.ipynb, ../../omicverse_guide/docs/Tutorials-single/t_preprocess_cpu.ipynb, ../../omicverse_guide/docs/Tutorials-single/t_preprocess_gpu.ipynb
  • 0Tools and files. 3 referenced file(s) missing: ../../omicverse_guide/docs/Tutorials-single/t_preprocess.ipynb, ../../omicverse_guide/docs/Tutorials-single/t_preprocess_cpu.ipynb, ../../omicverse_guide/docs/Tutorials-single/t_preprocess_gpu.ipynb
  • 0Result and completion. Does not say what the result is
  • 40Consistency. Frontmatter name (single-cell-preprocessing-with-omicverse) differs from the folder (single-preprocessing)
  • 50When it triggers. No condition that starts the skill
  • 50Failures and branches. 0 branches, has a failure section
  • 70Inputs and preconditions. Inputs and preconditions are listed
  • 85Steps. 41 steps, 1 vague phrases
  • 100Execution cost. Instruction body is 2766 tokens
  • 100Running it twice. No mutating operations
  • 100Progress reporting. Reports progress
  • medium Safety rules and hard prohibitions inside a skill: they belong in the system prompt, here they protect nothing

Everything here is measured from the skill text rather than judged by a model, so the numbers are checkable. A parameter weighs more when it is a more common reason for the process to stall.

Quality signals

  • +5Description has no quoted example phrases that should trigger the skill
  • +4Description does not say when NOT to use the skill (false activations)
  • +3Output format is not stated: the model decides each time
  • +1No license
  • +2Single-language instructions
  • +3Description length 180: enough signal without eating the budget
  • +4Structure: 11 headings
  • +3Step-by-step instructions: 41 items
  • +4Has examples (8 code blocks)

Quality base 70; lint remarks subtract, signals add up to 100. Result: 59.