Fix CVE-2026-44431 and CVE-2026-44432: pin urllib3>=2.7.0 #330
dpark01docker.yml
on: pull_request
get-version
7s
paths-filter
8s
Matrix: scan-containers
Matrix: deploy-to-quay
Annotations
19 warnings and 6 notices
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paths-filter
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: dorny/paths-filter@v3. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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build-baseimage-arm64
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: docker/build-push-action@v6. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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build-baseimage-amd64
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: docker/build-push-action@v6. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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build-core-arm64
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: docker/build-push-action@v6. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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build-core-amd64
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: docker/build-push-action@v6. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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build-classify-arm64
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: docker/build-push-action@v6. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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build-phylo-arm64
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: docker/build-push-action@v6. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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build-phylo-amd64
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: docker/build-push-action@v6. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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build-assemble-amd64
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: docker/build-push-action@v6. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Variables should be defined before their use:
docker/Dockerfile.assemble#L23
UndefinedVar: Usage of undefined variable '$PERL5LIB'
More info: https://docs.docker.com/go/dockerfile/rule/undefined-var/
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build-mega-arm64
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: docker/build-push-action@v6. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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test-core
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: codecov/codecov-action@v4. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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build-classify-amd64
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: docker/build-push-action@v6. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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build-mega-amd64
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: docker/build-push-action@v6. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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test-phylo
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: codecov/codecov-action@v4. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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test-classify
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: codecov/codecov-action@v4. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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build-assemble-arm64
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: docker/build-push-action@v6. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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Variables should be defined before their use:
docker/Dockerfile.assemble#L23
UndefinedVar: Usage of undefined variable '$PERL5LIB'
More info: https://docs.docker.com/go/dockerfile/rule/undefined-var/
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test-assemble
Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: codecov/codecov-action@v4. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/
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scan-containers (phylo)
Trivy found 0 findings for phylo (after policy filtering)
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scan-containers (baseimage)
Trivy found 0 findings for baseimage (after policy filtering)
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scan-containers (core)
Trivy found 0 findings for core (after policy filtering)
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scan-containers (assemble)
Trivy found 0 findings for assemble (after policy filtering)
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scan-containers (classify)
Trivy found 0 findings for classify (after policy filtering)
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scan-containers (mega)
Trivy found 0 findings for mega (after policy filtering)
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Artifacts
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broadinstitute~viral-ngs~25D8JK.dockerbuild
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119 KB |
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broadinstitute~viral-ngs~36D8L8.dockerbuild
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104 KB |
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broadinstitute~viral-ngs~JA1FAJ.dockerbuild
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sha256:4ec075d2261e18e8c3490642278c5686158cf7ad5bc01a7a69f6717aae4d5d5f
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broadinstitute~viral-ngs~K990RL.dockerbuild
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98.9 KB |
sha256:3b1a02242931798e909223a462efba5cb480ed805ed3057b48b39282974c58dc
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broadinstitute~viral-ngs~NNX7N2.dockerbuild
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113 KB |
sha256:1dc765aacb30be5ca039e330fd6f2bca226d525f6bbe30e4b9e67d3e1d862919
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broadinstitute~viral-ngs~NQAAK7.dockerbuild
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119 KB |
sha256:e3a73285284e49af9f1ac6ee5f13a06e37dcf4f9e8ddc646680d8ed18fc9ff3e
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broadinstitute~viral-ngs~SNKPFJ.dockerbuild
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broadinstitute~viral-ngs~U3UCFV.dockerbuild
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broadinstitute~viral-ngs~V8QUYL.dockerbuild
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broadinstitute~viral-ngs~WROETA.dockerbuild
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