The v0 series of google-github-actions/auth is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions: https://github.com/google-github-actions/auth

Java 17.0.6+10 build and test cloud

The v0 series of google-github-actions/setup-gcloud is no longer maintained. It will not receive updates, improvements, or security patches. Please upgrade to the latest supported versions: https://github.com/google-github-actions/setup-gcloud

WDL test RUN_CNN_WDL on cromwell

Process completed with exit code 1.

WDL test RUN_M2_WDL on cromwell

System.IO.IOException: No space left on device : '/home/runner/runners/2.317.0/_diag/Worker_20240802-172636-utc.log' at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset) at System.IO.Strategies.BufferedFileStreamStrategy.FlushWrite() at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder) at System.Diagnostics.TextWriterTraceListener.Flush() at GitHub.Runner.Common.HostTraceListener.WriteHeader(String source, TraceEventType eventType, Int32 id) at GitHub.Runner.Common.HostTraceListener.TraceEvent(TraceEventCache eventCache, String source, TraceEventType eventType, Int32 id, String message) at System.Diagnostics.TraceSource.TraceEvent(TraceEventType eventType, Int32 id, String message) at GitHub.Runner.Worker.Worker.RunAsync(String pipeIn, String pipeOut) at GitHub.Runner.Worker.Program.MainAsync(IHostContext context, String[] args) System.IO.IOException: No space left on device : '/home/runner/runners/2.317.0/_diag/Worker_20240802-172636-utc.log' at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset) at System.IO.Strategies.BufferedFileStreamStrategy.FlushWrite() at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder) at System.Diagnostics.TextWriterTraceListener.Flush() at GitHub.Runner.Common.HostTraceListener.WriteHeader(String source, TraceEventType eventType, Int32 id) at GitHub.Runner.Common.HostTraceListener.TraceEvent(TraceEventCache eventCache, String source, TraceEventType eventType, Int32 id, String message) at System.Diagnostics.TraceSource.TraceEvent(TraceEventType eventType, Int32 id, String message) at GitHub.Runner.Common.Tracing.Error(Exception exception) at GitHub.Runner.Worker.Program.MainAsync(IHostContext context, String[] args) Unhandled exception. System.IO.IOException: No space left on device : '/home/runner/runners/2.317.0/_diag/Worker_20240802-172636-utc.log' at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset) at System.IO.Strategies.BufferedFileStreamStrategy.FlushWrite() at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder) at System.Diagnostics.TextWriterTraceListener.Flush() at System.Diagnostics.TraceSource.Flush() at GitHub.Runner.Common.TraceManager.Dispose(Boolean disposing) at GitHub.Runner.Common.TraceManager.Dispose() at GitHub.Runner.Common.HostContext.Dispose(Boolean disposing) at GitHub.Runner.Common.HostContext.Dispose() at GitHub.Runner.Worker.Program.Main(String[] args)

Java 17.0.6+10 build and test unit

Java 17.0.6+10 build and test integration

Java 17.0.6+10 test on docker unit

Java 17.0.6+10 test on docker conda

Java 17.0.6+10 test on docker variantcalling

Java 17.0.6+10 test on docker integration

Validate script WDLs using womtools

The following actions uses Node.js version which is deprecated and will be forced to run on node20: actions/checkout@v3, actions/setup-java@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

Validate generated WDLs using womtools

WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell

You are running out of disk space. The runner will stop working when the machine runs out of disk space. Free space left: 8 MB

WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell

You are running out of disk space. The runner will stop working when the machine runs out of disk space. Free space left: 61 MB

WDL test RUN_CNV_SOMATIC_WDL on cromwell

WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell

Java 17.0.6+10 build and test cloud

The following actions uses Node.js version which is deprecated and will be forced to run on node20: actions/checkout@v3, actions/setup-java@v3, google-github-actions/auth@v0, google-github-actions/setup-gcloud@v0, actions/upload-artifact@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

WDL test RUN_CNN_WDL on cromwell

WDL test RUN_M2_WDL on cromwell

You are running out of disk space. The runner will stop working when the machine runs out of disk space. Free space left: 0 MB

Java 17.0.6+10 build and test unit

build and push gatk docker to artifacts

The following actions uses Node.js version which is deprecated and will be forced to run on node20: actions/checkout@v3, docker/metadata-action@v4, docker/setup-buildx-action@v2, docker/build-push-action@v4, actions/upload-artifact@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

Java 17.0.6+10 build and test integration

Java 17.0.6+10 test on docker unit

The following actions uses Node.js version which is deprecated and will be forced to run on node20: actions/checkout@v3, actions/setup-java@v3, google-github-actions/auth@v0, google-github-actions/setup-gcloud@v0, actions/download-artifact@v3, actions/upload-artifact@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

Java 17.0.6+10 test on docker conda

The following actions uses Node.js version which is deprecated and will be forced to run on node20: actions/checkout@v3, actions/setup-java@v3, google-github-actions/auth@v0, google-github-actions/setup-gcloud@v0, actions/download-artifact@v3, actions/upload-artifact@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

Java 17.0.6+10 test on docker variantcalling

The following actions uses Node.js version which is deprecated and will be forced to run on node20: actions/checkout@v3, actions/setup-java@v3, google-github-actions/auth@v0, google-github-actions/setup-gcloud@v0, actions/download-artifact@v3, actions/upload-artifact@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

Java 17.0.6+10 test on docker integration

The following actions uses Node.js version which is deprecated and will be forced to run on node20: actions/checkout@v3, actions/setup-java@v3, google-github-actions/auth@v0, google-github-actions/setup-gcloud@v0, actions/download-artifact@v3, actions/upload-artifact@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

Deprecation notice: v1, v2, and v3 of the artifact actions

The following artifacts were uploaded using a version of actions/upload-artifact that is scheduled for deprecation: "gatkDockerImage", "test-results-17.0.6+10-cloud", "test-results-17.0.6+10-integration", "test-results-17.0.6+10-unit", "test-results-docker-17.0.6+10-conda", "test-results-docker-17.0.6+10-integration", "test-results-docker-17.0.6+10-unit", "test-results-docker-17.0.6+10-variantcalling". Please update your workflow to use v4 of the artifact actions. Learn more: https://github.blog/changelog/2024-04-16-deprecation-notice-v3-of-the-artifact-actions/

Artifacts

Produced during runtime

Name	Size
gatkDockerImage	2.32 GB
test-results-17.0.6+10-cloud	333 KB
test-results-17.0.6+10-integration	3.46 MB
test-results-17.0.6+10-unit	157 MB
test-results-docker-17.0.6+10-conda	281 KB
test-results-docker-17.0.6+10-integration	3.37 MB
test-results-docker-17.0.6+10-unit	155 MB
test-results-docker-17.0.6+10-variantcalling	234 KB

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VCF AC/AF changes [VS-1366] #4529

Summary

VCF AC/AF changes [VS-1366] #4529

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gatk-tests.yml

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