eqtl-catalogue-region-fetch

Fetch a region of cis-eQTL summary statistics from EBI eQTL Catalogue v7+ via tabix-on-FTP. Use when an agent needs eQTL beta / SE / p-value for every variant in a window around a gene's TSS for one specific dataset (study × tissue × quantification method). Input: dataset_id, chromosome, start, end, optional molecular_trait_id. Output: harmonised TSV slice.

Quality

81%

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Passed

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Quality

Content

75%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

The body is action-rich with executable CLI, config schema, and realistic output examples, and the workflow is clearly sequenced for a read-only fetch. Its main weakness is progressive disclosure: multiple referenced bundle files (dataset index, demo input, the script itself) are absent from the skill, breaking the navigation the body promises.

Suggestions

Ship the referenced bundle files the body depends on, or remove/guard the references — the script at skills/eqtl-catalogue-region-fetch/eqtl_catalogue_region_fetch.py, data/dataset_index_r7.tsv, data/dataset_index_r7.provenance.json, and examples/input.json are all missing.

Tighten Gotcha #6: split the single long sentence with stacked parentheticals (33-of-758 probed, QTD000584 row counts) into a short rule plus a compact table or a one-line example, so the core guidance is not buried.

Make workflow validation explicit: add a checkpoint after the tabix fetch (e.g., 'verify n_variants > 0 and the expected columns are present before writing') rather than leaving verification implicit.

Dimension	Reasoning	Score
Conciseness	Mostly lean and assumes Claude's intelligence with no generic padding, but Gotchas #6 is a very dense run-on with stacked parenthetical statistics, and the Trigger 'Do NOT fire when' list overlaps the Scope section, leaving minor tightening opportunities.	4 / 5
Actionability	Fully executable guidance throughout: copy-paste CLI commands, a concrete JSON config schema, and realistic example outputs (manifest.yaml, variants.tsv rows, report.md) covering the common cases.	5 / 5
Workflow Clarity	A clearly sequenced 5-step workflow (Resolve dataset_id → Pick region → Tabix fetch → Filter by molecular_trait_id → Write outputs) with named error states; validation is mostly implicit rather than called out as explicit checkpoints, and it is a read-only fetch so the destructive cap does not apply.	4 / 5
Progressive Disclosure	Sections are well-organized, but the body repeatedly references bundled files that do not exist in the skill — data/dataset_index_r7.tsv, data/dataset_index_r7.provenance.json, examples/input.json, and skills/eqtl-catalogue-region-fetch/eqtl_catalogue_region_fetch.py — so navigation to those materials is broken.	2 / 5
	Total	15 / 20 Passed

Description

87%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

The description is specific, complete, and distinct: it names concrete actions, parameters, and outputs, and gives an explicit 'Use when' trigger tied to real user needs. Trigger-term coverage is strong but slightly technical, lacking a few plain synonyms.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions and parameters — 'Fetch a region of cis-eQTL summary statistics', 'via tabix-on-FTP', beta/SE/p-value, dataset_id/chromosome/start/end/molecular_trait_id, and 'harmonised TSV slice' as output — giving comprehensive coverage.	5 / 5
Completeness	Explicitly answers both 'what' ('Fetch a region of cis-eQTL summary statistics...') and 'when' ('Use when an agent needs eQTL beta / SE / p-value for every variant in a window around a gene's TSS'), plus concrete Input/Output specification.	5 / 5
Trigger Term Quality	Strong domain keywords ('cis-eQTL summary statistics', 'EBI eQTL Catalogue v7+', 'tabix-on-FTP', 'beta / SE / p-value', "window around a gene's TSS") that a bioinformatics user would say, but a few natural synonyms/extensions are absent.	4 / 5
Distinctiveness Conflict Risk	Highly specific niche — EBI eQTL Catalogue, tabix-on-FTP, one (study × tissue × quantification method) dataset — with distinct triggers and minimal overlap with other skills.	5 / 5
	Total	19 / 20 Passed

Validation

93%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 15 / 16 Passed

Validation for skill structure

Criteria	Description	Result
metadata_field	'metadata' should map string keys to string values	Warning

	Total	15 / 16 Passed

Repository: ClawBio/ClawBio
Path: skills/eqtl-catalogue-region-fetch/SKILL.md
Commit: d30153a

Reviewed: 3 days ago

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