BC tooluniverse-epigenomics
Production-ready genomics and epigenomics data processing for BixBench questions. Handles methylation array analysis (CpG filtering, differential methylation, age-related CpG detection, chromosome-level density), ChIP-seq peak analysis (peak calling, motif enrichment, coverage stats), ATAC-seq chromatin accessibility, multi-omics integration (expression + methylation correlation), and genome-wide statistics. Pure Python computation (pandas, scipy, numpy, pysam, statsmodels) plus ToolUniverse annotation tools (Ensembl, ENCODE, SCREEN, JASPAR, ReMap, RegulomeDB, ChIPAtlas). Supports BED, BigWig, methylation beta-value matrices, Illumina manifest files, and multi-sample clinical data. Use when processing methylation data, ChIP-seq peaks, ATAC-seq signals, or answering questions about CpG sites, differential methylation, chromatin accessibility, histone marks, or epigenomic statistics.
Production-ready genomics and epigenomics data processing for BixBench questions.
As a process C 55/100 · Has gaps — weak spots: inputs and preconditions, execution cost, running it twice
How to improve
- The SKILL.md body is over 5,000 tokens: move reference detail into references/ and load it when needed.
- 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 · 0
✓ No critical or high findings
Files scanned: 4. Evidence is masked. Grey chips explain why severity was lowered.
Against the Agent Skills spec
- warning
body-longSKILL.md body ≈ 13442 tokens (recommended < 5000); move details to references/
Process rating: all ten parameters 55/100
- 0Inputs and preconditions. Does not say what the process needs to start
- 0Progress reporting. Says nothing while it works
- 30Running it twice. 1 mutating operations with no state check
- 40Execution cost. Instruction body is 13442 tokens: crowds the task out of the window
- 50When it triggers. No condition that starts the skill
- 50Failures and branches. 0 branches, has a failure section
- 60Tools and files. Uses tools (python) that frontmatter does not declare
- 60Result and completion. Output format stated, no completion criterion
- 85Steps. 72 steps, 2 vague phrases
- 100Consistency. Name and required fields are in place
- 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
- +3Description length 894: 120–800 characters recommended
- +1No license
- +2Single-language instructions
- +4Description says when NOT to use the skill
- +4Structure: 52 headings
- +3Step-by-step instructions: 72 items
- +3Output format is stated explicitly
- +4Has examples (25 code blocks)
Quality base 70; lint remarks subtract, signals add up to 100. Result: 78.