{"id":234779,"url":"https://github.com/nextstrain/nextclade","last_synced_at":"2026-08-14T02:00:40.191Z","repository":{"id":36960034,"uuid":"271799467","full_name":"nextstrain/nextclade","owner":"nextstrain","description":"Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic 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1/8 approved changesets -- score normalized to 1","details":null,"documentation":{"short":"Determines if the project requires human code review before pull requests (aka merge requests) are merged.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#code-review"}},{"name":"Maintained","score":10,"reason":"30 commit(s) and 18 issue activity found in the last 90 days -- score normalized to 10","details":null,"documentation":{"short":"Determines if the project is \"actively maintained\".","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#maintained"}},{"name":"CII-Best-Practices","score":0,"reason":"no effort to earn an OpenSSF best practices badge detected","details":null,"documentation":{"short":"Determines if the project has an OpenSSF (formerly CII) Best Practices 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permissions found"],"documentation":{"short":"Determines if the project's workflows follow the principle of least privilege.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#token-permissions"}},{"name":"License","score":10,"reason":"license file detected","details":["Info: project has a license file: LICENSE:0","Info: FSF or OSI recognized license: MIT License: LICENSE:0"],"documentation":{"short":"Determines if the project has defined a license.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#license"}},{"name":"Signed-Releases","score":0,"reason":"Project has not signed or included provenance with any releases.","details":["Warn: release artifact 3.16.0 not signed: https://api.github.com/repos/nextstrain/nextclade/releases/237603796","Warn: release artifact 3.15.3 not signed: https://api.github.com/repos/nextstrain/nextclade/releases/230634566","Warn: release artifact 3.15.2 not signed: https://api.github.com/repos/nextstrain/nextclade/releases/229291107","Warn: release artifact 3.15.1 not signed: https://api.github.com/repos/nextstrain/nextclade/releases/226180930","Warn: release artifact 3.15.0 not signed: https://api.github.com/repos/nextstrain/nextclade/releases/224512777","Warn: release artifact 3.16.0 does not have provenance: https://api.github.com/repos/nextstrain/nextclade/releases/237603796","Warn: release artifact 3.15.3 does not have provenance: https://api.github.com/repos/nextstrain/nextclade/releases/230634566","Warn: release artifact 3.15.2 does not have provenance: https://api.github.com/repos/nextstrain/nextclade/releases/229291107","Warn: release artifact 3.15.1 does not have provenance: https://api.github.com/repos/nextstrain/nextclade/releases/226180930","Warn: release artifact 3.15.0 does not have provenance: https://api.github.com/repos/nextstrain/nextclade/releases/224512777"],"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"name":"Security-Policy","score":0,"reason":"security policy file not detected","details":["Warn: no security policy file detected","Warn: no security file to analyze","Warn: no security file to analyze","Warn: no security file to analyze"],"documentation":{"short":"Determines if the project has published a security policy.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#security-policy"}},{"name":"Binary-Artifacts","score":10,"reason":"no binaries found in the repo","details":null,"documentation":{"short":"Determines if the project has generated executable (binary) artifacts in the source repository.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#binary-artifacts"}},{"name":"Branch-Protection","score":0,"reason":"branch protection not enabled on development/release branches","details":["Warn: branch protection not enabled for branch 'master'"],"documentation":{"short":"Determines if the default and release branches are protected with GitHub's branch protection settings.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#branch-protection"}},{"name":"Fuzzing","score":0,"reason":"project is not fuzzed","details":["Warn: no fuzzer integrations found"],"documentation":{"short":"Determines if the project uses fuzzing.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#fuzzing"}},{"name":"Packaging","score":10,"reason":"packaging workflow detected","details":["Info: Project packages its releases by way of GitHub Actions.: .github/workflows/cli.yml:39"],"documentation":{"short":"Determines if the project is published as a package that others can easily download, install, easily update, and uninstall.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#packaging"}},{"name":"SAST","score":0,"reason":"SAST tool is not run on all commits -- score normalized to 0","details":["Warn: 0 commits out of 26 are checked with a SAST tool"],"documentation":{"short":"Determines if the project uses static code analysis.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#sast"}},{"name":"Pinned-Dependencies","score":0,"reason":"dependency not pinned by hash detected -- score normalized to 0","details":["Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/bioconda.yml:38: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/bioconda.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/builder-docker-image.yml:32: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/builder-docker-image.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/builder-docker-image.yml:35: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/builder-docker-image.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/builder-docker-image.yml:41: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/builder-docker-image.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/builder-docker-image.yml:52: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/builder-docker-image.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/cli.yml:209: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:212: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:222: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:231: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/cli.yml:260: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:263: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:278: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:383: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:389: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:420: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:426: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/cli.yml:438: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/cli.yml:58: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:76: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:86: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:97: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/cli.yml:129: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:144: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/cli.yml:326: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:329: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:335: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:354: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:360: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/cli.yml:158: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:161: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:171: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/cli.yml:180: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/cli.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/web.yml:36: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/web.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/web.yml:63: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/web.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/web.yml:73: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/web.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/web.yml:84: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/web.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/web.yml:97: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/web.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/web.yml:116: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/web.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/web.yml:147: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/web.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/web.yml:188: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/web.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/web.yml:194: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/web.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/web.yml:242: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/web.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/web.yml:247: update your workflow using https://app.stepsecurity.io/secureworkflow/nextstrain/nextclade/web.yml/master?enable=pin","Warn: containerImage not pinned by hash: docker/docker-dev.dockerfile:3","Warn: containerImage not pinned by hash: docker/docker-dev.dockerfile:290","Warn: containerImage not pinned by hash: docker/docker-dev.dockerfile:297","Warn: containerImage not pinned by hash: docker/docker-dev.dockerfile:304","Warn: containerImage not pinned by hash: docker/docker-dev.dockerfile:327","Warn: containerImage not pinned by hash: docker/docker-dev.dockerfile:340","Warn: containerImage not pinned by hash: docker/docker-dev.dockerfile:367","Warn: containerImage not pinned by hash: docker/docker-dev.dockerfile:390","Warn: containerImage not pinned by hash: docker/docker-dev.dockerfile:413","Warn: containerImage not pinned by hash: docker/docker-dev.dockerfile:430","Warn: containerImage not pinned by hash: docker/docker-dev.dockerfile:458","Warn: containerImage not pinned by hash: docker/docker-prod-alpine.dockerfile:1: pin your Docker image by updating alpine:3 to alpine:3@sha256:4bcff63911fcb4448bd4fdacec207030997caf25e9bea4045fa6c8c44de311d1","Warn: containerImage not pinned by hash: docker/docker-prod-debian.dockerfile:1: pin your Docker image by updating debian:11 to debian:11@sha256:8ec25a9073e8cc89a184a6256e219828196d75203375a8ad4f0977f3011f2115","Warn: containerImage not pinned by hash: docs/Dockerfile:1: pin your Docker image by updating continuumio/miniconda3 to continuumio/miniconda3@sha256:4a2425c3ca891633e5a27280120f3fb6d5960a0f509b7594632cdd5bb8cbaea8","Warn: containerImage not pinned by hash: paper/Dockerfile:1: pin your Docker image by updating openjournals/paperdraft to openjournals/paperdraft@sha256:97efb4fd37622244195e21df163e03a51b5e221452680957eaff4bfb97db8a46","Warn: pipCommand not pinned by hash: docker/docker-dev.dockerfile:166-167","Warn: npmCommand not pinned by hash: docker/docker-dev.dockerfile:189-194","Warn: downloadThenRun not pinned by hash: docker/docker-dev.dockerfile:209-215","Warn: pipCommand not pinned by hash: paper/Dockerfile:10-11","Info:   0 out of  32 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of  11 third-party GitHubAction dependencies pinned","Info:   1 out of  16 containerImage dependencies pinned","Info:   0 out of   2 pipCommand dependencies pinned","Info:   0 out of   1 npmCommand dependencies pinned","Info:   0 out of   1 downloadThenRun dependencies pinned"],"documentation":{"short":"Determines if the project has declared and pinned the dependencies of its build process.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#pinned-dependencies"}},{"name":"Vulnerabilities","score":0,"reason":"92 existing vulnerabilities detected","details":["Warn: Project is vulnerable to: GHSA-2rxc-gjrp-vjhx","Warn: Project is vulnerable to: RUSTSEC-2024-0404","Warn: Project is vulnerable to: RUSTSEC-2021-0145 / GHSA-g98v-hv3f-hcfr","Warn: Project is vulnerable to: RUSTSEC-2024-0375","Warn: Project is vulnerable to: RUSTSEC-2021-0141","Warn: Project is vulnerable to: RUSTSEC-2021-0142","Warn: Project is vulnerable to: RUSTSEC-2024-0421 / GHSA-h97m-ww89-6jmq","Warn: Project is vulnerable to: RUSTSEC-2024-0019 / GHSA-r8w9-5wcg-vfj7","Warn: Project is vulnerable to: RUSTSEC-2024-0436","Warn: Project is vulnerable to: RUSTSEC-2024-0370","Warn: Project is vulnerable to: GHSA-4p46-pwfr-66x6","Warn: Project is vulnerable to: RUSTSEC-2025-0009","Warn: Project is vulnerable to: GHSA-c86p-w88r-qvqr","Warn: Project is vulnerable to: GHSA-c827-hfw6-qwvm","Warn: Project is vulnerable to: GHSA-qg5g-gv98-5ffh","Warn: Project is vulnerable to: RUSTSEC-2024-0399","Warn: Project is vulnerable to: GHSA-rr8g-9fpq-6wmg","Warn: Project is vulnerable to: RUSTSEC-2025-0023","Warn: Project is vulnerable to: RUSTSEC-2023-0075 / GHSA-r24f-hg58-vfrw","Warn: Project is vulnerable to: GHSA-968p-4wvh-cqc8","Warn: Project is vulnerable to: GHSA-67hx-6x53-jw92","Warn: Project is vulnerable to: GHSA-7v5v-9h63-cj86","Warn: Project is vulnerable to: GHSA-wf5p-g6vw-rhxx","Warn: Project is vulnerable to: GHSA-jr5f-v2jv-69x6","Warn: Project is vulnerable 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