Skills gwas-database Audit History
📦

Audit History

gwas-database - 7 audits

Version comparison

Capability and finding changes across audited versions, newest first.

VersionDateResultReview itemsChange vs previous
v7 LatestJul 5, 2026, 06:00 PM 1 confirmed7No capability change
v6 Jul 5, 2026, 06:00 PM 1 confirmed7No capability change
v5 Jun 30, 2026, 05:45 AM 3 confirmed0No capability change
v4 Jan 17, 2026, 07:44 AM No confirmed findings0No capability change
v3 Jan 17, 2026, 07:44 AM No confirmed findings0No capability change
v2 Jan 12, 2026, 04:25 PM No confirmed findings0External commandsFilesystem access
v1 Jan 4, 2026, 04:35 PM No confirmed findings0Baseline

Jul 5, 2026, 06:00 PM

Most static findings are false positives from Markdown backticks and intended examples accessing public NHGRI-EBI GWAS endpoints. Confirmed risks are limited to FTP or plain HTTP summary-statistics downloads and local file writing without integrity or path safeguards. No prompt injection or malicious exfiltration language was found.

2
Files scanned
1,402
Lines analyzed
11
Review items
0
False positives ignored

Confirmed security concerns (1)

Medium
Unverified Summary Statistics Download
The skill includes workflows that fetch summary statistics over FTP or plain HTTP and save them locally without checksum or signature validation.
The cited examples use wget over FTP or requests against an http://ftp.ebi.ac.uk URL, then write downloaded bytes locally. The endpoint is legitimate, but the workflow lacks integrity verification.
Capability review items (7)

These are real local capabilities that may be expected for this skill, so they require review but are not counted as confirmed malicious behavior.

Medium
Python file write/append
with open(output_path, 'wb') as f:
The example writes streamed network content to a local path derived from parameters. Normal GCST IDs are structured, but the workflow lacks path validation, overwrite protection, and checksum checks.
Medium
FTP protocol
# ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCSTXXXXXX/
The skill recommends ftp:// access for GWAS summary statistics. FTP lacks transport security and integrity protection, so downloaded research data could be tampered with in transit.
Medium
FTP protocol
wget ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCSTXXXXXX/harmonised/GCSTXXXXXX-harm
The skill recommends ftp:// access for GWAS summary statistics. FTP lacks transport security and integrity protection, so downloaded research data could be tampered with in transit.
Low
Python HTTP libraries
response = requests.get(harmonised_url, stream=True)
This request streams a summary-statistics download built from a plain HTTP FTP mirror URL. The source is legitimate, but the example lacks secure transport and integrity validation.
Low
Hardcoded URL
ftp_base = "http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics"
This URL points to a plain HTTP or FTP bulk-download path for public summary statistics. The domain is legitimate, but the transport is not integrity protected.
Low
Hardcoded URL
1. **FTP download**: http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/
This URL points to a plain HTTP or FTP bulk-download path for public summary statistics. The domain is legitimate, but the transport is not integrity protected.
Low
Hardcoded URL
- **FTP site**: http://ftp.ebi.ac.uk/pub/databases/gwas/
This URL points to a plain HTTP or FTP bulk-download path for public summary statistics. The domain is legitimate, but the transport is not integrity protected.

Risk Factors

🌐 Network access (93)
references/api_reference.md:510 references/api_reference.md:63 references/api_reference.md:103 references/api_reference.md:155 references/api_reference.md:199 references/api_reference.md:237 references/api_reference.md:278 references/api_reference.md:303 references/api_reference.md:308 references/api_reference.md:365 references/api_reference.md:397 references/api_reference.md:513 references/api_reference.md:516 references/api_reference.md:520 references/api_reference.md:523 references/api_reference.md:526 references/api_reference.md:544 references/api_reference.md:578 references/api_reference.md:609 references/api_reference.md:614 references/api_reference.md:643 references/api_reference.md:652 references/api_reference.md:683 references/api_reference.md:714 references/api_reference.md:724 references/api_reference.md:769 references/api_reference.md:779 references/api_reference.md:28 references/api_reference.md:29 references/api_reference.md:102 references/api_reference.md:153 references/api_reference.md:198 references/api_reference.md:236 references/api_reference.md:271 references/api_reference.md:303 references/api_reference.md:318 references/api_reference.md:359 references/api_reference.md:390 references/api_reference.md:453 references/api_reference.md:461 references/api_reference.md:464 references/api_reference.md:540 references/api_reference.md:570 references/api_reference.md:606 references/api_reference.md:634 references/api_reference.md:647 references/api_reference.md:672 references/api_reference.md:761 SKILL.md:106 SKILL.md:116 SKILL.md:124 SKILL.md:132 SKILL.md:147 SKILL.md:167 SKILL.md:173 SKILL.md:198 SKILL.md:226 SKILL.md:253 SKILL.md:285 SKILL.md:290 SKILL.md:508 SKILL.md:49 SKILL.md:91 SKILL.md:92 SKILL.md:95 SKILL.md:96 SKILL.md:105 SKILL.md:114 SKILL.md:123 SKILL.md:131 SKILL.md:143 SKILL.md:163 SKILL.md:188 SKILL.md:219 SKILL.md:235 SKILL.md:251 SKILL.md:285 SKILL.md:303 SKILL.md:326 SKILL.md:331 SKILL.md:348 SKILL.md:412 SKILL.md:499 SKILL.md:565 SKILL.md:598 SKILL.md:599 SKILL.md:600 SKILL.md:601 SKILL.md:602 SKILL.md:603 SKILL.md:604 SKILL.md:258 SKILL.md:407
📁 Filesystem access (1)
⚙️ External commands (71)
Audited by: codex

Jul 5, 2026, 06:00 PM

Most static findings are false positives from Markdown backticks and intended examples accessing public NHGRI-EBI GWAS endpoints. Confirmed risks are limited to FTP or plain HTTP summary-statistics downloads and local file writing without integrity or path safeguards. No prompt injection or malicious exfiltration language was found.

2
Files scanned
1,402
Lines analyzed
11
Review items
0
False positives ignored

Confirmed security concerns (1)

Medium
Unverified Summary Statistics Download
The skill includes workflows that fetch summary statistics over FTP or plain HTTP and save them locally without checksum or signature validation.
The cited examples use wget over FTP or requests against an http://ftp.ebi.ac.uk URL, then write downloaded bytes locally. The endpoint is legitimate, but the workflow lacks integrity verification.
Capability review items (7)

These are real local capabilities that may be expected for this skill, so they require review but are not counted as confirmed malicious behavior.

Medium
Python file write/append
with open(output_path, 'wb') as f:
The example writes streamed network content to a local path derived from parameters. Normal GCST IDs are structured, but the workflow lacks path validation, overwrite protection, and checksum checks.
Medium
FTP protocol
# ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCSTXXXXXX/
The skill recommends ftp:// access for GWAS summary statistics. FTP lacks transport security and integrity protection, so downloaded research data could be tampered with in transit.
Medium
FTP protocol
wget ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCSTXXXXXX/harmonised/GCSTXXXXXX-harm
The skill recommends ftp:// access for GWAS summary statistics. FTP lacks transport security and integrity protection, so downloaded research data could be tampered with in transit.
Low
Python HTTP libraries
response = requests.get(harmonised_url, stream=True)
This request streams a summary-statistics download built from a plain HTTP FTP mirror URL. The source is legitimate, but the example lacks secure transport and integrity validation.
Low
Hardcoded URL
ftp_base = "http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics"
This URL points to a plain HTTP or FTP bulk-download path for public summary statistics. The domain is legitimate, but the transport is not integrity protected.
Low
Hardcoded URL
1. **FTP download**: http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/
This URL points to a plain HTTP or FTP bulk-download path for public summary statistics. The domain is legitimate, but the transport is not integrity protected.
Low
Hardcoded URL
- **FTP site**: http://ftp.ebi.ac.uk/pub/databases/gwas/
This URL points to a plain HTTP or FTP bulk-download path for public summary statistics. The domain is legitimate, but the transport is not integrity protected.

Risk Factors

🌐 Network access (93)
references/api_reference.md:510 references/api_reference.md:63 references/api_reference.md:103 references/api_reference.md:155 references/api_reference.md:199 references/api_reference.md:237 references/api_reference.md:278 references/api_reference.md:303 references/api_reference.md:308 references/api_reference.md:365 references/api_reference.md:397 references/api_reference.md:513 references/api_reference.md:516 references/api_reference.md:520 references/api_reference.md:523 references/api_reference.md:526 references/api_reference.md:544 references/api_reference.md:578 references/api_reference.md:609 references/api_reference.md:614 references/api_reference.md:643 references/api_reference.md:652 references/api_reference.md:683 references/api_reference.md:714 references/api_reference.md:724 references/api_reference.md:769 references/api_reference.md:779 references/api_reference.md:28 references/api_reference.md:29 references/api_reference.md:102 references/api_reference.md:153 references/api_reference.md:198 references/api_reference.md:236 references/api_reference.md:271 references/api_reference.md:303 references/api_reference.md:318 references/api_reference.md:359 references/api_reference.md:390 references/api_reference.md:453 references/api_reference.md:461 references/api_reference.md:464 references/api_reference.md:540 references/api_reference.md:570 references/api_reference.md:606 references/api_reference.md:634 references/api_reference.md:647 references/api_reference.md:672 references/api_reference.md:761 SKILL.md:106 SKILL.md:116 SKILL.md:124 SKILL.md:132 SKILL.md:147 SKILL.md:167 SKILL.md:173 SKILL.md:198 SKILL.md:226 SKILL.md:253 SKILL.md:285 SKILL.md:290 SKILL.md:508 SKILL.md:49 SKILL.md:91 SKILL.md:92 SKILL.md:95 SKILL.md:96 SKILL.md:105 SKILL.md:114 SKILL.md:123 SKILL.md:131 SKILL.md:143 SKILL.md:163 SKILL.md:188 SKILL.md:219 SKILL.md:235 SKILL.md:251 SKILL.md:285 SKILL.md:303 SKILL.md:326 SKILL.md:331 SKILL.md:348 SKILL.md:412 SKILL.md:499 SKILL.md:565 SKILL.md:598 SKILL.md:599 SKILL.md:600 SKILL.md:601 SKILL.md:602 SKILL.md:603 SKILL.md:604 SKILL.md:258 SKILL.md:407
📁 Filesystem access (1)
⚙️ External commands (71)
Audited by: codex

Jun 30, 2026, 05:45 AM

Static analysis flagged many Markdown backticks, URLs, and GWAS scientific notation as high-risk patterns, but these are largely documentation false positives. The real risks are legitimate public network access, an FTP/wget download example, and a local file write example for summary statistics, so publication is acceptable with a network and download warning.

2
Files scanned
1,402
Lines analyzed
6
Review items
1
False positives ignored

Confirmed security concerns (3)

Medium
Public Network Requests to GWAS Catalog APIs
The skill documents Python requests calls to NHGRI-EBI GWAS Catalog endpoints. This is expected for the skill, but it sends user-selected query terms, variant IDs, and trait IDs to an external public service.
The network calls are explicit and repeated, and the destination is the official GWAS Catalog domain. I did not find evidence that credentials or local secrets are collected or transmitted.
Medium
Bulk Summary Statistics Download Examples
The skill includes examples for downloading GWAS summary statistics with FTP or streamed HTTP. This can retrieve large files and should be run only when the user expects external downloads.
The download behavior is directly shown in documentation examples. It targets EBI public data, so the risk is operational rather than malicious.
Low
Local File Write in Download Helper Example
The reference documentation writes a downloaded compressed summary statistics file to a user-provided output directory. The pattern is expected for a downloader, but users should choose output paths deliberately.
The file write is explicit and limited to saving downloaded data. I did not find evidence of overwriting sensitive paths or writing executable content.
Static false positives ignored (1)

These static matches were dismissed by semantic review or matched schema-only tokens, so they are shown for transparency but do not drive the quality score.

Low
Static Backtick and Weak-Crypto Alerts Are Documentation False Positives
Many external command and weak cryptography alerts point to Markdown inline code, code fences, REST terminology, GWAS names, endpoint text, p-value notation, or HTTP status documentation rather than executable risky code.
Line-number review shows Markdown documentation and examples, not Ruby execution or cryptographic implementation. No executable skill script is present in the scanned files.

Detected Patterns

HTTP Client Calls in Example CodeShell Download Command Example
Audited by: codex

Jan 17, 2026, 07:44 AM

All 353 static findings are FALSE POSITIVES. This is a documentation-only skill containing no executable code. The static analyzer incorrectly flags Markdown code block backticks as shell commands, genetic research p-value notation (e.g., p=5e-8) as cryptographic algorithms, and the slug 'k-dense' as C2 keywords. The skill documents legitimate API queries to the public NHGRI-EBI GWAS Catalog maintained by EBI and NHGRI.

3
Files scanned
3,215
Lines analyzed
3
Review items
0
False positives ignored
Audited by: claude

Jan 17, 2026, 07:44 AM

All 353 static findings are FALSE POSITIVES. This is a documentation-only skill containing no executable code. The static analyzer incorrectly flags Markdown code block backticks as shell commands, genetic research p-value notation (e.g., p=5e-8) as cryptographic algorithms, and the slug 'k-dense' as C2 keywords. The skill documents legitimate API queries to the public NHGRI-EBI GWAS Catalog maintained by EBI and NHGRI.

3
Files scanned
3,215
Lines analyzed
3
Review items
0
False positives ignored
Audited by: claude

Jan 12, 2026, 04:25 PM

All 346 static findings are FALSE POSITIVES. This is a documentation-only skill containing no executable code. The static analyzer incorrectly flags Markdown code formatting backticks as shell commands and genetic research terms like 'pvalue' and 'beta' as cryptographic algorithms. The skill documents legitimate API queries to the public NHGRI-EBI GWAS Catalog.

2
Files scanned
1,400
Lines analyzed
3
Review items
0
False positives ignored

Risk Factors

⚙️ External commands (222)
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🌐 Network access (98)
references/api_reference.md:510 references/api_reference.md:63 references/api_reference.md:103 references/api_reference.md:155 references/api_reference.md:199 references/api_reference.md:237 references/api_reference.md:278 references/api_reference.md:303 references/api_reference.md:308 references/api_reference.md:365 references/api_reference.md:397 references/api_reference.md:513 references/api_reference.md:516 references/api_reference.md:520 references/api_reference.md:523 references/api_reference.md:526 references/api_reference.md:544 references/api_reference.md:578 references/api_reference.md:609 references/api_reference.md:614 references/api_reference.md:643 references/api_reference.md:652 references/api_reference.md:683 references/api_reference.md:714 references/api_reference.md:724 references/api_reference.md:769 references/api_reference.md:779 references/api_reference.md:28 references/api_reference.md:29 references/api_reference.md:102 references/api_reference.md:153 references/api_reference.md:198 references/api_reference.md:236 references/api_reference.md:271 references/api_reference.md:303 references/api_reference.md:318 references/api_reference.md:359 references/api_reference.md:390 references/api_reference.md:453 references/api_reference.md:461 references/api_reference.md:464 references/api_reference.md:540 references/api_reference.md:570 references/api_reference.md:606 references/api_reference.md:634 references/api_reference.md:647 references/api_reference.md:672 references/api_reference.md:761 references/api_reference.md:789 references/api_reference.md:790 references/api_reference.md:791 references/api_reference.md:792 references/api_reference.md:793 SKILL.md:106 SKILL.md:116 SKILL.md:124 SKILL.md:132 SKILL.md:147 SKILL.md:167 SKILL.md:173 SKILL.md:198 SKILL.md:226 SKILL.md:253 SKILL.md:285 SKILL.md:290 SKILL.md:508 SKILL.md:49 SKILL.md:91 SKILL.md:92 SKILL.md:95 SKILL.md:96 SKILL.md:105 SKILL.md:114 SKILL.md:123 SKILL.md:131 SKILL.md:143 SKILL.md:163 SKILL.md:188 SKILL.md:219 SKILL.md:235 SKILL.md:251 SKILL.md:285 SKILL.md:303 SKILL.md:326 SKILL.md:331 SKILL.md:348 SKILL.md:412 SKILL.md:499 SKILL.md:565 SKILL.md:598 SKILL.md:599 SKILL.md:600 SKILL.md:601 SKILL.md:602 SKILL.md:603 SKILL.md:604 SKILL.md:258 SKILL.md:407
📁 Filesystem access (1)
Audited by: claude

Jan 4, 2026, 04:35 PM

The skill contains documentation and example queries for public GWAS Catalog APIs and FTP downloads. No credential access, environment harvesting, or executable payload patterns were found.

5
Files scanned
1,400
Lines analyzed
1
Review items
0
False positives ignored
Audited by: claude