Changed flow allele filtering in Mutect2 to work separately on the tumor and the normal samples #4504
ilyasoifergatk-tests.yml
on: pull_request
check if the environment has privileges
0s
build and push gatk docker to artifacts
3m 5s
Validate script WDLs using womtools
2m 28s
Validate generated WDLs using womtools
2m 33s
Matrix: wdlTests
Matrix: test
Matrix: testOnDocker
Annotations
11 errors and 14 warnings
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Validate script WDLs using womtools
Process completed with exit code 1.
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Validate generated WDLs using womtools
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Java 17.0.6+10 build and test cloud
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Java 17.0.6+10 build and test unit
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build and push gatk docker to artifacts
buildx failed with: ERROR: failed to solve: process "/bin/sh -c ls . && rm /etc/apt/sources.list.d/google-cloud-sdk.list && apt update && apt-key list && curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - && add-apt-repository universe && apt update && apt-get --assume-yes install git-lfs && apt-get -y clean && apt-get -y autoclean && apt-get -y autoremove && rm -rf /var/lib/apt/lists/* && git lfs install --force && git lfs pull --include src/main/resources/large && export GRADLE_OPTS=\"-Xmx4048m -Dorg.gradle.daemon=false\" && /gatk/gradlew clean collectBundleIntoDir shadowTestClassJar shadowTestJar -Drelease=$RELEASE && cp -r $( find /gatk/build -name \"*bundle-files-collected\" )/ /gatk/unzippedJar/ && unzip -o -j $( find /gatk/unzippedJar -name \"gatkPython*.zip\" ) -d /gatk/unzippedJar/scripts && chmod -R a+rw /gatk/unzippedJar" did not complete successfully: exit code: 1
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WDL test RUN_CNV_SOMATIC_WDL on cromwell
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WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
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WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
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Java 17.0.6+10 build and test integration
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WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
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WDL test RUN_M2_WDL on cromwell
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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/
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Validate generated 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/
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Java 17.0.6+10 build and test cloud
No files were found with the provided path: build/reports/tests. No artifacts will be uploaded.
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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, 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/
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Java 17.0.6+10 build and test unit
No files were found with the provided path: build/reports/tests. No artifacts will be uploaded.
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Java 17.0.6+10 build and test 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, 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/
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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. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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WDL test RUN_CNV_SOMATIC_WDL on cromwell
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/
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WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
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/
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WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
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/
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Java 17.0.6+10 build and test integration
No files were found with the provided path: build/reports/tests. No artifacts will be uploaded.
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Java 17.0.6+10 build and test 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, 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/
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WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
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/
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WDL test RUN_M2_WDL on cromwell
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/
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