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BC latchbio-integration

Builds, registers, debugs, and operates bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake, programmatic execution, and Latch MCP. Use when authoring or deploying Latch workflows, configuring resources or interfaces, moving data, integrating Registry, or launching and monitoring runs.

K-Dense-AI/claude-scientific-skills Agent Skills author: K-Dense-AI MIT 11 files · 1 script body ≈ 2 309 tokens Open the sourcegithub.com↗ analyzed 12 h ago

Builds, registers, debugs, and operates bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake…

As a process C 61/100 · Has gaps — weak spots: result and completion, inputs and preconditions, running it twice

ProcedureSoftware developmenttype 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
B
94/100
safety, quality, tests
Safety 60%
95
Quality 40%
92
Run on models
none yet
Process rating
C
61/100
Has gaps
Result and completion w 14
0
Inputs and preconditions w 11
0
Running it twice w 4
30
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.

Broad scope 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 asks for more than the task needs: broad tool access, credential environment variables, binaries. Every extra permission widens the damage from a mistake or a compromise.

For the author

Narrow allowed-tools and the variable list to the minimum; replace binaries with readable sources or scripts.

How to improve

    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 Broad scope meta-broad-allowed-tools SKILL.md:1
      Broad tool permissions pre-approved: Bash
      allowed-tools: Read Write Edit Bash

    Files scanned: 11. Evidence is masked. Grey chips explain why severity was lowered.

    Against the Agent Skills spec

    • note edit-residue the text marks something as outdated (lines 41, 129, 179): check that old rules are not kept next to new ones — the full check reads the text for contradictions

    Process rating: all ten parameters 61/100

    • 0Result and completion. Does not say what the result is
    • 0Inputs and preconditions. Does not say what the process needs to start
    • 30Running it twice. 5 mutating operations with no state check
    • 50When it triggers. No condition that starts the skill
    • 50Failures and branches. 0 branches, has a failure section
    • 100Tools and files. Tools declared in frontmatter
    • 100Steps. 42 steps
    • 100Consistency. Name and required fields are in place
    • 100Execution cost. Instruction body is 2309 tokens
    • 100Progress reporting. Reports progress
    • low 11 top-level sections: this looks like several domains in one skill

    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
    • +2Single-language instructions
    • +3Description length 340: enough signal without eating the budget
    • +4Structure: 12 headings
    • +3Step-by-step instructions: 42 items
    • +4Has examples (10 code blocks)
    • +4Reference files are cited in the instructions (9 of 9)
    • +3All 1 scripts are documented
    • +1License stated

    Quality base 70; lint remarks subtract, signals add up to 100. Result: 92.