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Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.

FreedomIntelligence/OpenClaw-Medical-Skills Agent Skills author: FreedomIntelligence 22 files · 10 scripts body ≈ 2 104 tokens Open the sourcegithub.com↗ analyzed 14 h ago

Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data.

As a process C 53/100 · Has gaps — weak spots: result and completion, inputs and preconditions, running it twice

ProcedureDockerInfrastructuretype 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
86/100
safety, quality, tests
Safety 60%
82
Quality 40%
92
Run on models
none yet
Process rating
C
53/100
Has gaps
Result and completion w 14
0
Inputs and preconditions w 11
0
Progress reporting w 2
0
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

    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 · 6

    ✓ No critical or high findings

    Medium and low: 6
    • medium Dangerous commands cmd-pipe-to-shell references/installation.md:15
      Downloads and executes remote code from an unrecognised host (pipe to shell) (the skill's own vendor host)
      curl -s https://get.nextflow.io | bash
      vendor-host
    • medium Dangerous commands cmd-shell-rc references/installation.md:56
      Writes to a shell startup file
      echo 'export NXF_SINGULARITY_CACHEDIR="$HOME/.singularity/cache"' >> ~/.bashrc
    • medium Dangerous commands cmd-shell-rc references/installation.md:94
      Writes to a shell startup file
      echo 'export PATH="$HOME/bin:$PATH"' >> ~/.bashrc
    • low Dangerous commands cmd-background-process references/installation.md:29
      Starts a background / autostarted process
      sudo systemctl enable --now docker
    • low Dangerous commands cmd-pipe-to-shell scripts/check_environment.py:120
      Downloads and executes remote code from an unrecognised host (pipe to shell) (string literal in code, not executed; the skill's own vendor host)
      fix="curl -s https://get.nextflow.io | bash && mv nextflow ~/bin/ && export PATH=$HOME/bin:$PATH"
      code literalvendor-host
    • low Dangerous commands cmd-pipe-to-shell SKILL.md:75
      Downloads and executes remote code from an unrecognised host (pipe to shell) (documentation table row; the skill's own vendor host)
      | Not installed | `curl -s https://get.nextflow.io \| bash && mv nextflow ~/bin/` |
      tablevendor-host

    Files scanned: 22. 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 185): check that old rules are not kept next to new ones — the full check reads the text for contradictions

    Process rating: all ten parameters 53/100

    • 0Result and completion. Does not say what the result is
    • 0Inputs and preconditions. Does not say what the process needs to start
    • 0Progress reporting. Says nothing while it works
    • 30Running it twice. 3 mutating operations with no state check
    • 55Failures and branches. 1 branches
    • 60Tools and files. Uses tools (bash, web) that frontmatter does not declare
    • 70When it triggers. States when to use, but not when not to
    • 85Steps. 33 steps, 1 vague phrases
    • 100Consistency. Name and required fields are in place
    • 100Execution cost. Instruction body is 2104 tokens
    • low 13 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 359: enough signal without eating the budget
    • +4Structure: 26 headings
    • +3Step-by-step instructions: 33 items
    • +4Has examples (16 code blocks)
    • +4Reference files are cited in the instructions (3 of 3)
    • +3All 5 scripts are documented
    • +1License stated

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