{"$schema":"https://verifymcp.io/schemas/trust-report.json","schemaVersion":1,"license":{"name":"CC BY-NC 4.0","url":"https://creativecommons.org/licenses/by-nc/4.0/"},"generatedAt":"2026-11-05T18:24:45.673Z","url":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena","markdownUrl":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena.md","server":{"slug":"pipeworx-io-ena","name":"Ena","registryName":"io.github.pipeworx-io/ena","description":"European Nucleotide Archive (ENA) — EMBL-EBI's public record of raw sequencing runs, assemblies…","registryStatus":"active","deletedAt":null,"statusMessage":null,"liveness":"live","publisher":{"class":"unknown","claimed":false}},"component":{"slug":"pipeworx-mcp-ena","type":"npm","identifier":"@pipeworx/mcp-ena","withdrawn":false,"url":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena","version":"0.2.1","transport":"stdio","scoredAt":"2026-11-05T00:24:39.458Z"},"score":{"total":81,"tier":"high trust","status":"scored","weekDelta":3,"history":[{"date":"2026-11-05","total":81},{"date":"2026-11-04","total":81},{"date":"2026-11-03","total":81},{"date":"2026-11-02","total":80},{"date":"2026-11-01","total":65},{"date":"2026-10-31","total":78},{"date":"2026-10-30","total":78},{"date":"2026-10-29","total":78}]},"categories":[{"name":"Supply Chain Security","score":100,"verdict":"pass","reasons":["No malware found by supply-chain analysis.","No known CVEs affecting this package version or its production dependencies.","No install/post-install scripts declared.","No production dependencies, so there is no dependency health to assess."],"codes":[{"code":"supplychain.malware_clean","args":{}},{"code":"cve.none","args":{}},{"code":"installscript.none","args":{}},{"code":"dephealth.no_dependencies","args":{"deps":"0","unhealthy":"0"}}]},{"name":"Provenance & Transparency","score":97,"verdict":"fail","reasons":["Source repository is publicly reachable at the declared URL.","Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-ena).","Clear OSI-approved license (MIT).","Actively maintained (last published 3 days ago).","Disclosure check failed: no security disclosure policy was found in the source repository."],"codes":[{"code":"provenance.repo_verified","args":{}},{"code":"provenance.verified","args":{"repo":"pipeworx-io/mcp-ena"}},{"code":"license.osi","args":{"spdx":"MIT"}},{"code":"maintenance.recent","args":{"age_days":"3"}},{"code":"disclosure.absent","args":{}}]},{"name":"Schema Quality & AI Usability","score":60,"verdict":"fail","reasons":["AI-judged instruction clarity (good).","Context-footprint check failed: tool/resource definitions use about 868 tokens (~289/item across 3 items; 3 tools + 0 resources), over budget; trim descriptions and params.","Usage-examples check failed: none of the tools include examples."],"codes":[{"code":"schema.ai_quality","args":{"band":"good"}},{"code":"schema.footprint_heavy","args":{"avg":"289","items":"3","tools":"3","tokens":"868","resources":"0"}},{"code":"schema.examples_absent","args":{}}]},{"name":"Stability & Change Management","score":23,"verdict":"partial","reasons":["Stability observed for 7 of 30 days with no destabilising changes; credit accrues until the full window elapses."],"codes":[{"code":"stability.building_history","args":{"days":"7"}}]},{"name":"Tool Coverage","score":100,"verdict":"pass","reasons":["100% of tools have a non-trivial description (not blank, and not just the tool's name).","100% of tool parameters carry a description."],"codes":[{"code":"toolquality.descriptions","args":{"pct":"100"}},{"code":"toolquality.param_docs","args":{"pct":"100"}}]},{"name":"Tool Safety","score":100,"verdict":"pass","reasons":["No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.","We read all 3 captured tool definition(s), and no name or description among them implies an irreversible operation.","An AI judge read all 4 captured unit(s) of tool text and found none that tries to manipulate the model reading it."],"codes":[{"code":"toolsafety.injection_clean","args":{}},{"code":"toolsafety.destructive_none","args":{"tools":"3"}},{"code":"toolsafety.manipulation_clean","args":{"units":"4","judged":"4"}}]},{"name":"Capabilities","score":100,"verdict":"pass","reasons":["Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28."],"codes":[{"code":"protocol.supported","args":{"latest":"2026-07-28","version":"2025-11-25"}}]}],"inconclusive":[],"malware":[],"components":[{"slug":"ena-mcp","type":"remote","identifier":"https://gateway.pipeworx.io/ena/mcp","withdrawn":false,"score":77,"current":false,"url":"https://verifymcp.io/servers/pipeworx-io-ena/ena-mcp","markdownUrl":"https://verifymcp.io/servers/pipeworx-io-ena/ena-mcp.md"},{"slug":"pipeworx-mcp-ena","type":"npm","identifier":"@pipeworx/mcp-ena","withdrawn":false,"score":81,"current":true,"url":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena","markdownUrl":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena.md"}],"facts":[{"label":"Registry","value":"npm"},{"label":"Package","value":"@pipeworx/mcp-ena"},{"label":"Version","value":"0.2.1"},{"label":"Transport","value":"stdio"}],"install":{"available":true,"bundleSha256":null},"tools":[{"name":"ena_search","title":null,"description":"Search the European Nucleotide Archive for sequencing runs, studies, samples, assemblies or annotated sequence using ENA's own query grammar. AUTHORITATIVE for \"which public sequencing data exists for this organism / disease / country / platform\" — ENA is an INSDC partner, so it covers data deposited to NCBI SRA and DDBJ as well. PREFER OVER WEB SEARCH for any question about what raw sequence data has been deposited. Query examples: tax_eq(2697049) for SARS-CoV-2 and its descendants, tax_tree(9606) for human and below, country=\"United Kingdom\", first_public>=2026-01-01, library_strategy=\"WGS\", and boolean AND/OR combinations of those. Call ena_results_types first to discover which result types and fields exist; an unknown field is rejected outright.","inputs":[{"name":"fields","type":"string","required":false,"description":"Comma-separated columns to return. Omit for a sensible default set for the result type — an explicit empty value would return the accession column alone. Valid names per result type come from ena_res…"},{"name":"limit","type":"number","required":false,"description":"Maximum rows, 1-1000 (default 25). Note: upstream treats 0 as unlimited; this tool does not pass 0 through."},{"name":"query","type":"string","required":false,"description":"ENA query expression, e.g. tax_eq(2697049), tax_tree(9606) AND library_strategy=\"WGS\", country=\"Kenya\" AND first_public>=2025-01-01. Omit to list the newest records of the result type."},{"name":"result","type":"string","required":false,"description":"ENA result type to search. Common: read_run (raw sequencing runs), study, sample, experiment, analysis, assembly, sequence. Defaults to read_run. Full list from ena_results_types."},{"name":"sortFields","type":"string","required":false,"description":"Comma-separated columns to sort by."}],"outputs":[],"hasOutputSchema":false,"hasExamples":false,"tokenEstimate":388},{"name":"ena_filereport","title":null,"description":"List every sequencing data file behind an ENA accession, with direct FASTQ/BAM/CRAM download URLs, byte sizes and MD5 checksums. AUTHORITATIVE for \"where do I actually download the reads for this study/run/sample\" — give it a study accession (PRJEB37886, PRJNA…), run (ERR…, SRR…, DRR…), sample (SAMEA…, SAMN…) or experiment, and it returns one row per run with its files. The multi-file semicolon-separated upstream fields are split into arrays here, so a caller does not silently fetch only the first mate of a paired-end run.","inputs":[{"name":"accession","type":"string","required":true,"description":"ENA/INSDC accession: study (PRJEB37886, PRJNA…), run (ERR…/SRR…/DRR…), sample (SAMEA…/SAMN…), experiment (ERX…/SRX…) or taxon id. Must match the pattern the chosen result type accepts."},{"name":"fields","type":"string","required":false,"description":"Comma-separated columns. Omit for a file-oriented default set (URLs, sizes, checksums)."},{"name":"limit","type":"number","required":false,"description":"Maximum rows, 1-1000 (default 25)."},{"name":"result","type":"string","required":false,"description":"Result type to report files for. Default read_run; also analysis, assembly, wgs_set."}],"outputs":[],"hasOutputSchema":false,"hasExamples":false,"tokenEstimate":284},{"name":"ena_results_types","title":null,"description":"List every ENA result type you can search — with its live record count and last-updated date — and, for one named result type, every field you may query or return. This is the schema-discovery step for ena_search: ENA rejects an unknown or wrong-result-type field name outright, so reading the field list first is cheaper than guessing. Also useful on its own for \"how much public sequence data exists right now\" — the counts are the archive's live totals.","inputs":[{"name":"result","type":"string","required":false,"description":"Optional result type (e.g. read_run, study, sample) to also list its searchable/returnable fields. Omit to list result types only."}],"outputs":[],"hasOutputSchema":false,"hasExamples":false,"tokenEstimate":145}],"toolsTruncatedAtCapture":false,"diagnostics":{"capturedAt":"2026-11-05T00:24:39.000Z","track":"package","endpoint":null,"declaredUrl":null,"truncated":false,"tls":null,"dnssec":null,"auth":null,"httpsRedirect":null,"transports":[],"provenance":{"outcome":"verified","label":"Verified","reason":"verified","reasonLabel":"Verified","discovery":"attestation_endpoint","discoveryLabel":"Registry attestation endpoint","sourceRepo":null,"attestationSkipped":null,"attestationSkippedLabel":null},"installScripts":[],"installScriptsTotal":null,"vulnerabilities":[],"vulnerabilitiesTotal":null,"dependencies":{"nodes":0,"partial":false,"deprecated":null,"stale":null,"noRepo":null}},"mismatches":[],"changelog":{"trackingSince":"2026-10-29","recent":[{"id":"chg_01a19ed8-26ad-78d5-96ae-66dbd91e15c1","kind":"score.total_changed","summary":"Trust score (80 → 81)","materiality":"functional","direction":"improvement","scoreDelta":1,"occurredOn":"2026-11-03","url":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena#chg-chg_01a19ed8-26ad-78d5-96ae-66dbd91e15c1"},{"id":"chg_01a199a6-37f3-7730-a003-f5522170afa3","kind":"score.total_changed","summary":"Trust score (65 → 80)","materiality":"functional","direction":"improvement","scoreDelta":15,"occurredOn":"2026-11-02","url":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena#chg-chg_01a199a6-37f3-7730-a003-f5522170afa3"},{"id":"chg_01a199a6-37f2-7006-9b6b-5e486fcdebed","kind":"check.reverified","summary":"Malware scan (unverified → pass)","materiality":"security","direction":"improvement","scoreDelta":null,"occurredOn":"2026-11-02","url":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena#chg-chg_01a199a6-37f2-7006-9b6b-5e486fcdebed"},{"id":"chg_01a198ed-af59-757e-a797-dc59a3fc1bf1","kind":"check.reverified","summary":"Stability (unverified → 0.10)","materiality":"functional","direction":"improvement","scoreDelta":null,"occurredOn":"2026-11-01","url":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena#chg-chg_01a198ed-af59-757e-a797-dc59a3fc1bf1"},{"id":"chg_01a198ed-af5a-7657-b5e3-9fee2624557a","kind":"score.total_changed","summary":"Trust score (34 → 65)","materiality":"functional","direction":"improvement","scoreDelta":31,"occurredOn":"2026-11-01","url":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena#chg-chg_01a198ed-af5a-7657-b5e3-9fee2624557a"},{"id":"chg_01a198ea-e019-721d-9dc8-87117b397f0b","kind":"check.reason","summary":"Stability (Stability not yet verified: we do not have a sandbox capture of the MCP schema this version of the package serves yet.)","materiality":"security","direction":"neutral","scoreDelta":null,"occurredOn":"2026-11-01","url":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena#chg-chg_01a198ea-e019-721d-9dc8-87117b397f0b"},{"id":"chg_01a198ea-e01b-7d5c-86f1-b4926d2174da","kind":"score.total_changed","summary":"Trust score (78 → 34)","materiality":"functional","direction":"regression","scoreDelta":-44,"occurredOn":"2026-11-01","url":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena#chg-chg_01a198ea-e01b-7d5c-86f1-b4926d2174da"},{"id":"chg_01a198ea-e01b-73be-8888-50c5661f888a","kind":"package.version_changed","summary":"Package version (0.2.0 → 0.2.1)","materiality":"functional","direction":"neutral","scoreDelta":null,"occurredOn":"2026-11-01","url":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena#chg-chg_01a198ea-e01b-73be-8888-50c5661f888a"},{"id":"chg_01a198ea-e01a-7db5-a592-f8bd83c80f9f","kind":"check.appeared","summary":"First check of Schema quality (unverified)","materiality":"functional","direction":"neutral","scoreDelta":null,"occurredOn":"2026-11-01","url":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena#chg-chg_01a198ea-e01a-7db5-a592-f8bd83c80f9f"},{"id":"chg_01a198ea-e01a-7468-9d28-50f65d6a79c9","kind":"check.unverifiable","summary":"Tool coverage (100 → unverified)","materiality":"functional","direction":"regression","scoreDelta":null,"occurredOn":"2026-11-01","url":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena#chg-chg_01a198ea-e01a-7468-9d28-50f65d6a79c9"},{"id":"chg_01a198ea-e019-7dd0-9ca1-d504a2e08645","kind":"check.unverifiable","summary":"Capabilities (pass → unverified)","materiality":"functional","direction":"regression","scoreDelta":null,"occurredOn":"2026-11-01","url":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena#chg-chg_01a198ea-e019-7dd0-9ca1-d504a2e08645"},{"id":"chg_01a198ea-e018-74c6-901a-7af703e8aed4","kind":"check.unverifiable","summary":"Tool safety (pass → unverified)","materiality":"security","direction":"regression","scoreDelta":null,"occurredOn":"2026-11-01","url":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena#chg-chg_01a198ea-e018-74c6-901a-7af703e8aed4"},{"id":"chg_01a198ea-e016-7006-8529-78b9e28060e7","kind":"check.unverifiable","summary":"Malware scan (pass → unverified)","materiality":"security","direction":"regression","scoreDelta":null,"occurredOn":"2026-11-01","url":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena#chg-chg_01a198ea-e016-7006-8529-78b9e28060e7"},{"id":"chg_01a18a24-1c89-73fd-8c18-0bf1f63328a0","kind":"check.reverified","summary":"Security disclosure (unverified → fail)","materiality":"functional","direction":"regression","scoreDelta":null,"occurredOn":"2026-10-30","url":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena#chg-chg_01a18a24-1c89-73fd-8c18-0bf1f63328a0"},{"id":"chg_01a18674-e2c1-7996-b7b2-f93db5049161","kind":"score.first_scored","summary":"First indexed and scored","materiality":"functional","direction":"neutral","scoreDelta":null,"occurredOn":"2026-10-29","url":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena#chg-chg_01a18674-e2c1-7996-b7b2-f93db5049161"}],"truncated":false,"feedUrl":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena/changelog.json"},"links":{"html":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena","markdown":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena.md","changelogJson":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena/changelog.json","changelogRss":"https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena.xml","external":[{"label":"npm package","href":"https://www.npmjs.com/package/@pipeworx/mcp-ena"},{"label":"Socket report","href":"https://socket.dev/npm/package/@pipeworx/mcp-ena"},{"label":"Repository","href":"https://github.com/pipeworx-io/mcp-ena"},{"label":"Website","href":"https://pipeworx.io/packs/ena"}]}}