From 761297be8f32700906726449995c1dfd82820788 Mon Sep 17 00:00:00 2001 From: jamesemery Date: Thu, 21 Apr 2022 13:56:33 -0400 Subject: [PATCH] Replace Travis with GithubActions (#7754) * Switched over to using GithubActions for CI services and re-implemented our existing tests as github an actions workflow. Removed old Travis infrastructure and scripts. Co-authored-by: Louis Bergelson , James Emery --- .github/actions/install-cromwell/action.yml | 19 + .../upload-gatk-test-results/action.yml | 93 +++++ .github/workflows/gatk-tests.yml | 339 ++++++++++++++++++ .../run_cnn_variant_wdl.sh | 8 +- .../jsons/cnn_score_variants_travis.json | 24 +- .../jsons/cnn_score_variants_travis_1d.json | 24 +- .../jsons/cram2filtered_travis.json | 14 +- .../cnv_germline_case_scattered_workflow.json | 28 +- .../cnv_germline_cohort_workflow.json | 30 +- .../germline/run_cnv_germline_workflows.sh | 19 +- .../cnv_somatic_pair_wes_do-gc_workflow.json | 20 +- ...ic_pair_wes_do-gc_workflow_funcotator.json | 22 +- ...ic_pair_wes_no-gc_tumor_only_workflow.json | 16 +- .../cnv_somatic_pair_wes_no-gc_workflow.json | 20 +- ...ic_pair_wgs_do-gc_tumor_only_workflow.json | 16 +- .../cnv_somatic_pair_wgs_do-gc_workflow.json | 20 +- .../cnv_somatic_pair_wgs_no-gc_workflow.json | 20 +- .../cnv_somatic_panel_wes_do-gc_workflow.json | 16 +- .../cnv_somatic_panel_wes_no-gc_workflow.json | 16 +- .../cnv_somatic_panel_wgs_do-gc_workflow.json | 16 +- .../cnv_somatic_panel_wgs_no-gc_workflow.json | 16 +- .../somatic/run_cnv_somatic_workflows.sh | 38 +- scripts/github_actions/README.md | 1 + .../{travis => github_actions}/Reporter.py | 23 +- scripts/m2_cromwell_tests/pair_list | 4 +- .../m2_cromwell_tests/pair_list_tumor_only | 4 +- scripts/m2_cromwell_tests/run_m2_wdl.sh | 12 +- .../m2_cromwell_tests/test_m2_wdl_multi.json | 12 +- .../test_mitochondria_m2_wdl.json | 46 +-- scripts/travis/README.md | 1 - scripts/travis/check_for_pull_request | 4 - .../install_and_authenticate_to_gcloud.sh | 14 - scripts/travis/install_gcloud.sh | 10 - 33 files changed, 695 insertions(+), 270 deletions(-) create mode 100644 .github/actions/install-cromwell/action.yml create mode 100644 .github/actions/upload-gatk-test-results/action.yml create mode 100644 .github/workflows/gatk-tests.yml create mode 100644 scripts/github_actions/README.md rename scripts/{travis => github_actions}/Reporter.py (72%) delete mode 100644 scripts/travis/README.md delete mode 100755 scripts/travis/check_for_pull_request delete mode 100755 scripts/travis/install_and_authenticate_to_gcloud.sh delete mode 100755 scripts/travis/install_gcloud.sh diff --git a/.github/actions/install-cromwell/action.yml b/.github/actions/install-cromwell/action.yml new file mode 100644 index 00000000000..db26a6af992 --- /dev/null +++ b/.github/actions/install-cromwell/action.yml @@ -0,0 +1,19 @@ +name: 'install-cromwell' +description: 'installs cromwell and womtool locally for jobs that require it (and sets their paths as environment variables)' +inputs: + CROMWELL_VERSION: # id of input + description: 'Cromwell Version to download' + required: true +runs: + using: "composite" + steps: + - name: Set Cromwell env variables + run: | + echo "CROMWELL_JAR=${HOME}/cromwell-${{ inputs.CROMWELL_VERSION }}.jar" >> $GITHUB_ENV; + echo "WOMTOOL_JAR=${HOME}/womtool-${{ inputs.CROMWELL_VERSION }}.jar" >> $GITHUB_ENV; + shell: bash + - name: Download Cromwell and Womtools + run: | + wget -q -O $CROMWELL_JAR https://github.com/broadinstitute/cromwell/releases/download/${{ inputs.CROMWELL_VERSION }}/cromwell-${{ inputs.CROMWELL_VERSION }}.jar; + wget -q -O $WOMTOOL_JAR https://github.com/broadinstitute/cromwell/releases/download/${{ inputs.CROMWELL_VERSION }}/womtool-${{ inputs.CROMWELL_VERSION }}.jar; + shell: bash \ No newline at end of file diff --git a/.github/actions/upload-gatk-test-results/action.yml b/.github/actions/upload-gatk-test-results/action.yml new file mode 100644 index 00000000000..62166d4c64f --- /dev/null +++ b/.github/actions/upload-gatk-test-results/action.yml @@ -0,0 +1,93 @@ +name: 'upload-gatk-test-results' +description: 'Uploads the results for matrix runs of gatk-tests.yml and maybe comments on failing runs on the PR associated with the test' +inputs: + warnPR: + description: 'If true this will add a comment about the jococo tests to the PR with a link to the failed test' + required: true + job-matrix-id: + description: 'The job-unique identifier for which test was run (numbered by matrix run)' + required: true + repo-path: + description: 'The job-unique identifier to use for uploading the results of this run into a google bucket' + required: true + is-docker: + description: 'Whether to label the uplaod artifact as coming from a docker test' + required: false + identifier: + description: 'Identifier to use for finding the unique name for jobs in order to determine html logs location (eg. "Java 8 build and test integration")' + required: true +## Secrets and token inputs + repo-token: + description: 'The GITHUB_TOKEN secret used for querying the github api to locate the logs for this run' + required: false + bot-comment-key: + description: 'Key corresponding to the user account to be used for making comments on github about test failures' + required: false +## option to skip all but the artifact uplaod + only-artifact: + description: 'if "true" this will skip any uploading steps that require permissions and only upload the artifact file' + required: false + default: 'false' + +runs: + using: "composite" + steps: + - name: Upload test results + if: always() + uses: actions/upload-artifact@v2 + with: + # ternary expression syntax is workaround found here https://github.com/actions/runner/issues/409 + name: test-results-${{ inputs.is-docker == 'true' && 'docker-' || '' }}${{ matrix.Java }}-${{ matrix.testType }} + path: build/reports/tests + + - name: Upload to codecov + run: bash <(curl -s https://raw.githubusercontent.com/broadinstitute/codecov-bash-uploader/main/codecov-verified.bash) + shell: bash + + - name: Upload Reports + if: ${{ inputs.only-artifact != 'true' }} + id: uploadreports + run: | + gsutil -m cp -z html -z js -z xml -z css -r build/reports/tests gs:/${{ env.HELLBENDER_TEST_LOGS }}${{ inputs.repo-path }}/; + VIEW_URL=https://storage.googleapis.com${{ env.HELLBENDER_TEST_LOGS }}${{ inputs.repo-path }}/tests/test/index.html + echo "See the test report at ${VIEW_URL}"; + echo ::set-output name=view_url::"${VIEW_URL}" + shell: bash + +# This code is necessary in order to extract the URL for the logs for a particular run. The github context exposes the run_id object +# which corresponds to the unique identifier for an individual workflow execution but it doesn't expose the job_id.id which is necessary +# to extract the logs for failing jobs. The best workaround seems to be this approach (querying the API and parsing the json output). + - name: Extract Log Location + if: ${{ inputs.only-artifact != 'true' }} + id: loghtml + env: + GITHUB_TOKEN: ${{ inputs.repo-token }} + run: | + GITHUB_BASEURL=https://api.github.com + REPO_ID=$(curl --get -Ss -H "Authorization: token ${GITHUB_TOKEN}" -H "Accept: application/vnd.github.v3+json" https://api.github.com/repos/${{ github.repository }} | jq -r .id) + GITHUB_API="/repositories/${REPO_ID}/actions/runs/${{ github.run_id }}/jobs" + eval "$(curl --get -Ss -H "Authorization: token ${GITHUB_TOKEN}" -H "Accept: application/vnd.github.v3+json" "${GITHUB_BASEURL}${GITHUB_API}?per_page=30" \ + | jq -r --arg job_name "${{ inputs.identifier }}" '.jobs | map(select(.name == $job_name)) | .[0] | @sh "job_id=\(.id) html_url=\(.html_url)"')" + + echo ::set-output name=job_id::"${job_id}" + echo ::set-output name=html_url::"${html_url}" + echo ${job_id} + echo ${html_url} + shell: bash + + - name: Updating the PR with failed results + if: ${{ inputs.warnPR == 'true' && inputs.only-artifact != 'true' }} + env: + GITHUB_TOKEN: ${{ inputs.bot-comment-key }} + TEST_TYPE: ${{ matrix.testType }} + GITHUB_EVENT_NUMBER: ${{ github.event.number }} + GITHUB_REPOSITORY: ${{ github.repository }} + JOB_MATRIX_ID: ${{ inputs.job-matrix-id }} + GITHUB_RUN_ID: ${{ github.run_id }} + JDK_VERSION: ${{ matrix.Java }} + ACTIONS_JOB_WEB_URL: https://github.com/${{github.repository}}/actions/runs/${{github.run_id}} + GITHUB_LOGS_URL: ${{ steps.loghtml.outputs.html_url }} + run: | + pip install --user PyGithub; + python scripts/github_actions/Reporter.py ${{ steps.uploadreports.outputs.view_url }}; + shell: bash \ No newline at end of file diff --git a/.github/workflows/gatk-tests.yml b/.github/workflows/gatk-tests.yml new file mode 100644 index 00000000000..4fd19452523 --- /dev/null +++ b/.github/workflows/gatk-tests.yml @@ -0,0 +1,339 @@ +name: Build and Test GATK 4 +on: + push: + branches: + - 'master' + pull_request: + workflow_dispatch: + +env: + CROMWELL_VERSION: 51 + TERM: dumb + GRADLE_OPTS: "-Xmx2048m -Dorg.gradle.daemon=false" + HELLBENDER_TEST_INPUTS: gs://hellbender/test/resources/ + HELLBENDER_TEST_STAGING: gs://hellbender-test-logs/staging/ + HELLBENDER_TEST_LOGS: /hellbender-test-logs/build_reports/ + HELLBENDER_TEST_PROJECT: broad-dsde-dev + TEST_VERBOSITY: minimal + REGISTRY: ghcr.io + IMAGE_NAME: ${{ github.repository }} + +jobs: + ## This workaround is necessary since there is no equivalent to the old TRAVIS_SECURE_ENVIRONMENT variable that indicated + ## if a run was privileged and had secrets. Since the GCP credentials are necessary for all tests in order to upload their, + ## results that makes them a reasonable proxy for testing the credentials of this entire execution. https://github.com/actions/runner/issues/520 + check-secrets: + name: check if the environment has privileges + outputs: + google-credentials: ${{ steps.google-credentials.outputs.defined }} + runs-on: ubuntu-latest + steps: + - id: google-credentials + env: + GCP_CREDENTIALS: ${{ secrets.GCP_CREDENTIALS }} + if: "${{ env.GCP_CREDENTIALS != '' }}" + run: echo "::set-output name=defined::true" + + + buildDocker: + name: build and push gatk docker to artifacts + runs-on: ubuntu-latest + steps: + - name: checkout gatk + uses: actions/checkout@v2 + + - name: Extract metadata (tags, labels) for Docker + id: meta + uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 + with: + images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} + tags: | + type=raw,value=${{github.sha}} + + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@v1 + + - name: Build and push Docker image + uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc + with: + context: . + tags: ${{ steps.meta.outputs.tags }} + labels: ${{ steps.meta.outputs.labels }} + outputs: type=docker,dest=/tmp/myimage.tar + # By uploading the docker image as an artifact we save ourselves the requirement for the image to be built with ghcr push permission + - name: Upload docker image as artifact + uses: actions/upload-artifact@v2 + with: + name: gatkDockerImage + path: /tmp/myimage.tar + + #Run our non-docker tests + test: + runs-on: ubuntu-latest + needs: check-secrets + strategy: + matrix: + java: [ 8, 11 ] + experimental: [ false ] + scalaVersion: [ 2.11, 2.12 ] + testType: [ cloud, integration, unit ] + exclude: + - java: 11 + scalaVersion: 2.11 + - java: 8 + scalaVersion: 2.12 + - java: 8 + testType: integration + - java: 8 + testType: unit + fail-fast: false + continue-on-error: ${{ matrix.experimental }} + env: + TEST_TYPE: ${{ matrix.testType }} + SCALA_VERSION: ${{ matrix.scalaVersion }} + name: Java ${{ matrix.Java }} build and test ${{ matrix.testType }} + steps: + - uses: actions/checkout@v2 + with: + fetch-depth: 0 + - name: 'Set up java ${{ matrix.Java }}' + uses: actions/setup-java@v2 + with: + java-version: ${{ matrix.Java }} + distribution: 'adopt' + cache: gradle + + - name: 'Compile with Gradle' + run: | + ./gradlew compileJava ; ./gradlew installDist + + #Google Cloud stuff + - id: 'gcloud-auth' + if: needs.check-secrets.outputs.google-credentials == 'true' + uses: google-github-actions/auth@v0 + with: + credentials_json: ${{ secrets.GCP_CREDENTIALS }} + project_id: ${{ env.HELLBENDER_TEST_PROJECT }} + create_credentials_file: true + + - name: "export the credentials for GATK tests" + if: needs.check-secrets.outputs.google-credentials == 'true' + run: echo "HELLBENDER_JSON_SERVICE_ACCOUNT_KEY=${{ steps.auth.outputs.credentials_file_path }}" >> $GITHUB_ENV + + - name: 'Set up Cloud SDK' + if: needs.check-secrets.outputs.google-credentials == 'true' + uses: google-github-actions/setup-gcloud@v0 + + - name: pull lfs files + run: git lfs pull + + - name: compile test code + run: ./gradlew compileTestJava + + - name: run-tests + if: ${{ needs.check-secrets.outputs.google-credentials == 'true' || matrix.testType != 'cloud'}} + id: jacoco-tests + run: | + ./gradlew -Dscala.version=${{ env.SCALA_VERSION }} jacocoTestReport + + - uses: ./.github/actions/upload-gatk-test-results + if: always() + with: + warnPR: ${{ github.event_name == 'pull_request' && steps.jacoco-tests.outcome != 'success' }} + repo-token: ${{ secrets.GITHUB_TOKEN }} + job-matrix-id: ${{ github.run_id }}.1${{ strategy.job-index }} + repo-path: ${{ github.ref_name }}_${{ github.run_id }}.1${{ strategy.job-index }} + bot-comment-key: ${{ secrets.GATK_BOT_COMMENT_KEY }} + identifier: Java ${{ matrix.Java }} build and test ${{ matrix.testType }} + only-artifact: ${{ needs.check-secrets.outputs.google-credentials != 'true' }} + + + #Run our docker tests + testOnDocker: + needs: [buildDocker, check-secrets] + runs-on: ubuntu-latest + strategy: + matrix: + java: [ 8 ] + experimental: [ false ] + scalaVersion: [ 2.11 ] + testType: [ integration, unit, variantcalling, conda ] + fail-fast: false + continue-on-error: ${{ matrix.experimental }} + env: + TEST_TYPE: ${{ matrix.testType }} + SCALA_VERSION: ${{ matrix.scalaVersion }} + + name: Java ${{ matrix.Java }} test on docker ${{matrix.testType}} + steps: + - uses: actions/checkout@v2 + with: + fetch-depth: 0 #TODO make this shallow + + - name: 'Set up java ${{ matrix.Java }}' + uses: actions/setup-java@v2 + with: + java-version: ${{ matrix.Java }} + distribution: 'adopt' + cache: gradle + + #Google Cloud stuff + - id: 'gcloud-auth' + uses: google-github-actions/auth@v0 + if: needs.check-secrets.outputs.google-credentials == 'true' + with: + credentials_json: ${{ secrets.GCP_CREDENTIALS }} + project_id: ${{ env.HELLBENDER_TEST_PROJECT }} + create_credentials_file: true + + - name: "export the credentials for GATK tests" + if: needs.check-secrets.outputs.google-credentials == 'true' + run: echo "HELLBENDER_JSON_SERVICE_ACCOUNT_KEY=${{ steps.auth.outputs.credentials_file_path }}" >> $GITHUB_ENV + + - name: 'Set up Cloud SDK' + if: needs.check-secrets.outputs.google-credentials == 'true' + uses: google-github-actions/setup-gcloud@v0 + + - name: build test jars + run: ./gradlew clean shadowTestClassJar shadowTestJar + + - name: set up test folders and links + run: | + mkdir ./testJars; + echo $( find ./build/libs/ -name "gatk*test.jar"); + cp -r $( find ./build/libs/ -name "gatk*test.jar" ) ./testJars; + cp -r $( find ./build/libs/ -name "gatk*testDependencies.jar" ) ./testJars; + mkdir -p build/reports/; + chmod -R a+w build/reports/; + cp scripts/docker/dockertest.gradle . + + - name: Download docker image artifact + uses: actions/download-artifact@v2 + with: + name: gatkDockerImage + path: /tmp + - name: Load Docker image + run: | + docker load --input /tmp/myimage.tar + docker image ls -a + + - name: pull lfs files + run: git lfs pull + + - name: run-docker-tests + id: docker-jacocco-tests + run: | + docker run \ + -v $(pwd):/gatkCloneMountPoint:cached \ + -v $(pwd)/testJars:/jars:cached \ + --rm \ + -e "scala.version=${SCALA_VERSION}" \ + -e "TEST_VERBOSITY=minimal" \ + -e "TEST_TYPE=${TEST_TYPE}" \ + -t ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ github.sha }} \ + bash --init-file /gatk/gatkenv.rc /root/run_unit_tests.sh; + TEST_EXIT_VALUE=$?; + $( exit ${TEST_EXIT_VALUE} ); + sudo chmod -R a+w build/reports/; + mkdir build/reports/tests/test \ + && cp -rp build/reports/tests/testOnPackagedReleaseJar/* build/reports/tests/test \ + && rm -r build/reports/tests/testOnPackagedReleaseJar; + + - uses: ./.github/actions/upload-gatk-test-results + if: always() + with: + warnPR: ${{ github.event_name == 'pull_request' && steps.docker-jacocco-tests.outcome != 'success' }} + is-docker: true + repo-token: ${{ secrets.GITHUB_TOKEN }} + job-matrix-id: ${{ github.run_id }}.${{ strategy.job-index }} + repo-path: ${{ github.ref_name }}_${{ github.run_id }}.${{ strategy.job-index }} + bot-comment-key: ${{ secrets.GATK_BOT_COMMENT_KEY }} + identifier: Java ${{ matrix.Java }} test on docker ${{matrix.testType}} + only-artifact: ${{ needs.check-secrets.outputs.google-credentials != 'true' }} + + + #test wdl auto generation + wdlGen: + runs-on: ubuntu-latest + name: Test WDL Generation + steps: + - uses: actions/checkout@v2 + with: + fetch: 0 + - name: Set up java 8 + uses: actions/setup-java@v2 + with: + java-version: '8' + distribution: 'adopt' + cache: gradle + - uses: ./.github/actions/install-cromwell + with: + CROMWELL_VERSION: ${{ env.CROMWELL_VERSION }} + + - name: Run WDL Generation Test + run: ./gradlew gatkWDLGenValidation + + + #Run our various targeted medium scale wdl wiring tests + wdlTests: + runs-on: ubuntu-latest + strategy: + matrix: + wdlTest: [ 'RUN_CNV_GERMLINE_COHORT_WDL', 'RUN_CNV_GERMLINE_CASE_WDL', 'RUN_CNV_SOMATIC_WDL', 'RUN_M2_WDL', 'RUN_CNN_WDL' ] + continue-on-error: true + name: WDL test ${{ matrix.wdlTest }} on cromwell + steps: + - uses: actions/checkout@v2 + with: + fetch-depth: 0 + - name: pull lfs files + run: git lfs pull + - name: Set up java 8 + uses: actions/setup-java@v2 + with: + java-version: '8' + distribution: 'adopt' + cache: gradle + - uses: ./.github/actions/install-cromwell + with: + CROMWELL_VERSION: ${{ env.CROMWELL_VERSION }} + + - name: "Exporting Environment Variables for Wdl Scripts" + run: | + if [[ "${{ github.event_name }}" == "pull_request" ]] + then + echo "CI_PULL_REQUEST=${{ github.event.number }}" >> $GITHUB_ENV + fi + echo "CI_COMMIT=${{ github.sha }}" >> $GITHUB_ENV + + - name: "CNV_GERMLINE_COHORT_WDL_TEST" + if: ${{ matrix.wdlTest == 'RUN_CNV_GERMLINE_COHORT_WDL' }} + run: | + echo "Running CNV germline cohort workflow"; + bash scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh COHORT; + + - name: "CNV_GERMLINE_CASE_WDL_TEST" + if: ${{ matrix.wdlTest == 'RUN_CNV_GERMLINE_CASE_WDL' }} + run: | + echo "Running CNV germline case workflow"; + bash scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh CASE; + + - name: "CNV_SOMATIC_WDL_TEST" + if: ${{ matrix.wdlTest == 'RUN_CNV_SOMATIC_WDL' }} + run: | + echo "Running CNV somatic workflows"; + bash scripts/cnv_cromwell_tests/somatic/run_cnv_somatic_workflows.sh; + + - name: "M2_WDL_TEST" + if: ${{ matrix.wdlTest == 'RUN_M2_WDL' }} + run: | + echo "Deleting some unused files before running M2 WDL..."; + rm -Rf src/test/resources/large/VQSR; + echo "Running M2 WDL"; + bash scripts/m2_cromwell_tests/run_m2_wdl.sh; + + - name: "CNN_WDL_TEST" + if: ${{ matrix.wdlTest == 'RUN_CNN_WDL' }} + run: | + echo "Running CNN WDL"; + bash scripts/cnn_variant_cromwell_tests/run_cnn_variant_wdl.sh; diff --git a/scripts/cnn_variant_cromwell_tests/run_cnn_variant_wdl.sh b/scripts/cnn_variant_cromwell_tests/run_cnn_variant_wdl.sh index fd7ba3355e6..18a4d824c3d 100644 --- a/scripts/cnn_variant_cromwell_tests/run_cnn_variant_wdl.sh +++ b/scripts/cnn_variant_cromwell_tests/run_cnn_variant_wdl.sh @@ -4,7 +4,7 @@ set -e script_path=$( cd "$(dirname "${BASH_SOURCE}")" ; pwd -P ) cd "$script_path" -WORKING_DIR=/home/travis/build/broadinstitute +WORKING_DIR=/home/runner/work/gatk set -e echo "Building docker image for CNN WDL tests (skipping unit tests)..." @@ -14,12 +14,12 @@ echo "Building docker without running unit tests... =========" cd $WORKING_DIR/gatk # IMPORTANT: This code is duplicated in the cnv and M2 WDL test. -if [ ${TRAVIS_PULL_REQUEST} != false ]; then +if [ ! -z "$CI_PULL_REQUEST" ]; then HASH_TO_USE=FETCH_HEAD - sudo bash build_docker.sh -e ${HASH_TO_USE} -s -u -d $PWD/temp_staging/ -t ${TRAVIS_PULL_REQUEST}; + sudo bash build_docker.sh -e ${HASH_TO_USE} -s -u -d $PWD/temp_staging/ -t ${CI_PULL_REQUEST}; echo "using fetch head:"$HASH_TO_USE else - HASH_TO_USE=${TRAVIS_COMMIT} + HASH_TO_USE=${CI_COMMIT} sudo bash build_docker.sh -e ${HASH_TO_USE} -s -u -d $PWD/temp_staging/; echo "using travis commit:"$HASH_TO_USE fi diff --git a/scripts/cnn_variant_wdl/jsons/cnn_score_variants_travis.json b/scripts/cnn_variant_wdl/jsons/cnn_score_variants_travis.json index ce3fd2bd701..83439b5143d 100755 --- a/scripts/cnn_variant_wdl/jsons/cnn_score_variants_travis.json +++ b/scripts/cnn_variant_wdl/jsons/cnn_score_variants_travis.json @@ -1,21 +1,21 @@ { - "CNNScoreVariantsWorkflow.bam_file": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/VQSR/g94982_b37_chr20_1m_895_bamout.bam", - "CNNScoreVariantsWorkflow.bam_file_index": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/VQSR/g94982_b37_chr20_1m_895_bamout.bai", - "CNNScoreVariantsWorkflow.calling_intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/VQSR/contig20_1m_10m.interval_list", + "CNNScoreVariantsWorkflow.bam_file": "/home/runner/work/gatk/gatk/src/test/resources/large/VQSR/g94982_b37_chr20_1m_895_bamout.bam", + "CNNScoreVariantsWorkflow.bam_file_index": "/home/runner/work/gatk/gatk/src/test/resources/large/VQSR/g94982_b37_chr20_1m_895_bamout.bai", + "CNNScoreVariantsWorkflow.calling_intervals": "/home/runner/work/gatk/gatk/src/test/resources/large/VQSR/contig20_1m_10m.interval_list", "CNNScoreVariantsWorkflow.gatk_docker": "__GATK_DOCKER__", - "CNNScoreVariantsWorkflow.input_vcf": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/VQSR/g94982_b37_chr20_1m_895.vcf.gz", - "CNNScoreVariantsWorkflow.input_vcf_index": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/VQSR/g94982_b37_chr20_1m_895.vcf.gz.tbi", + "CNNScoreVariantsWorkflow.input_vcf": "/home/runner/work/gatk/gatk/src/test/resources/large/VQSR/g94982_b37_chr20_1m_895.vcf.gz", + "CNNScoreVariantsWorkflow.input_vcf_index": "/home/runner/work/gatk/gatk/src/test/resources/large/VQSR/g94982_b37_chr20_1m_895.vcf.gz.tbi", "CNNScoreVariantsWorkflow.output_prefix": "g94982_b37_chr20_1m_895", - "CNNScoreVariantsWorkflow.reference_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta", - "CNNScoreVariantsWorkflow.reference_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/human_g1k_v37.20.21.dict", - "CNNScoreVariantsWorkflow.reference_fasta_index": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta.fai", + "CNNScoreVariantsWorkflow.reference_fasta": "/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta", + "CNNScoreVariantsWorkflow.reference_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.dict", + "CNNScoreVariantsWorkflow.reference_fasta_index": "/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta.fai", "CNNScoreVariantsWorkflow.resources": [ - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/VQSR/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.20.1M-10M.vcf", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/VQSR/Omni25_sites_1525_samples.b37.20.1M-10M.vcf" + "/home/runner/work/gatk/gatk/src/test/resources/large/VQSR/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.20.1M-10M.vcf", + "/home/runner/work/gatk/gatk/src/test/resources/large/VQSR/Omni25_sites_1525_samples.b37.20.1M-10M.vcf" ], "CNNScoreVariantsWorkflow.resources_index": [ - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/VQSR/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.20.1M-10M.vcf.idx", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/VQSR/Omni25_sites_1525_samples.b37.20.1M-10M.vcf.idx" + "/home/runner/work/gatk/gatk/src/test/resources/large/VQSR/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.20.1M-10M.vcf.idx", + "/home/runner/work/gatk/gatk/src/test/resources/large/VQSR/Omni25_sites_1525_samples.b37.20.1M-10M.vcf.idx" ], "CNNScoreVariantsWorkflow.inference_batch_size": "1", "CNNScoreVariantsWorkflow.transfer_batch_size": "2", diff --git a/scripts/cnn_variant_wdl/jsons/cnn_score_variants_travis_1d.json b/scripts/cnn_variant_wdl/jsons/cnn_score_variants_travis_1d.json index af221aa5bf6..dc1ec66f4f5 100755 --- a/scripts/cnn_variant_wdl/jsons/cnn_score_variants_travis_1d.json +++ b/scripts/cnn_variant_wdl/jsons/cnn_score_variants_travis_1d.json @@ -1,21 +1,21 @@ { - "CNNScoreVariantsWorkflow.bam_file": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/VQSR/g94982_b37_chr20_1m_895_bamout.bam", - "CNNScoreVariantsWorkflow.bam_file_index": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/VQSR/g94982_b37_chr20_1m_895_bamout.bai", - "CNNScoreVariantsWorkflow.calling_intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/VQSR/contig20_1m_10m.interval_list", + "CNNScoreVariantsWorkflow.bam_file": "/home/runner/work/gatk/gatk/src/test/resources/large/VQSR/g94982_b37_chr20_1m_895_bamout.bam", + "CNNScoreVariantsWorkflow.bam_file_index": "/home/runner/work/gatk/gatk/src/test/resources/large/VQSR/g94982_b37_chr20_1m_895_bamout.bai", + "CNNScoreVariantsWorkflow.calling_intervals": "/home/runner/work/gatk/gatk/src/test/resources/large/VQSR/contig20_1m_10m.interval_list", "CNNScoreVariantsWorkflow.gatk_docker": "__GATK_DOCKER__", - "CNNScoreVariantsWorkflow.input_vcf": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/VQSR/g94982_b37_chr20_1m_895.vcf.gz", - "CNNScoreVariantsWorkflow.input_vcf_index": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/VQSR/g94982_b37_chr20_1m_895.vcf.gz.tbi", + "CNNScoreVariantsWorkflow.input_vcf": "/home/runner/work/gatk/gatk/src/test/resources/large/VQSR/g94982_b37_chr20_1m_895.vcf.gz", + "CNNScoreVariantsWorkflow.input_vcf_index": "/home/runner/work/gatk/gatk/src/test/resources/large/VQSR/g94982_b37_chr20_1m_895.vcf.gz.tbi", "CNNScoreVariantsWorkflow.output_prefix": "g94982_b37_chr20_1m_895", - "CNNScoreVariantsWorkflow.reference_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta", - "CNNScoreVariantsWorkflow.reference_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/human_g1k_v37.20.21.dict", - "CNNScoreVariantsWorkflow.reference_fasta_index": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta.fai", + "CNNScoreVariantsWorkflow.reference_fasta": "/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta", + "CNNScoreVariantsWorkflow.reference_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.dict", + "CNNScoreVariantsWorkflow.reference_fasta_index": "/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta.fai", "CNNScoreVariantsWorkflow.resources": [ - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/VQSR/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.20.1M-10M.vcf", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/VQSR/Omni25_sites_1525_samples.b37.20.1M-10M.vcf" + "/home/runner/work/gatk/gatk/src/test/resources/large/VQSR/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.20.1M-10M.vcf", + "/home/runner/work/gatk/gatk/src/test/resources/large/VQSR/Omni25_sites_1525_samples.b37.20.1M-10M.vcf" ], "CNNScoreVariantsWorkflow.resources_index": [ - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/VQSR/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.20.1M-10M.vcf.idx", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/VQSR/Omni25_sites_1525_samples.b37.20.1M-10M.vcf.idx" + "/home/runner/work/gatk/gatk/src/test/resources/large/VQSR/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.20.1M-10M.vcf.idx", + "/home/runner/work/gatk/gatk/src/test/resources/large/VQSR/Omni25_sites_1525_samples.b37.20.1M-10M.vcf.idx" ], "CNNScoreVariantsWorkflow.inference_batch_size": "1", "CNNScoreVariantsWorkflow.transfer_batch_size": "2", diff --git a/scripts/cnn_variant_wdl/jsons/cram2filtered_travis.json b/scripts/cnn_variant_wdl/jsons/cram2filtered_travis.json index f0bacc0570d..f7f07f50cd7 100755 --- a/scripts/cnn_variant_wdl/jsons/cram2filtered_travis.json +++ b/scripts/cnn_variant_wdl/jsons/cram2filtered_travis.json @@ -1,16 +1,16 @@ { - "Cram2FilteredVcf.input_file": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram", - "Cram2FilteredVcf.reference_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta", - "Cram2FilteredVcf.reference_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/human_g1k_v37.20.21.dict", - "Cram2FilteredVcf.reference_fasta_index": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta.fai", - "Cram2FilteredVcf.resources" : ["/home/travis/build/broadinstitute/gatk/src/test/resources/large/dbsnp_138.b37.20.21.vcf"], - "Cram2FilteredVcf.resources_index" : ["/home/travis/build/broadinstitute/gatk/src/test/resources/large/dbsnp_138.b37.20.21.vcf.idx"], + "Cram2FilteredVcf.input_file": "/home/runner/work/gatk/gatk/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram", + "Cram2FilteredVcf.reference_fasta": "/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta", + "Cram2FilteredVcf.reference_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.dict", + "Cram2FilteredVcf.reference_fasta_index": "/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta.fai", + "Cram2FilteredVcf.resources" : ["/home/runner/work/gatk/gatk/src/test/resources/large/dbsnp_138.b37.20.21.vcf"], + "Cram2FilteredVcf.resources_index" : ["/home/runner/work/gatk/gatk/src/test/resources/large/dbsnp_138.b37.20.21.vcf.idx"], "Cram2FilteredVcf.output_prefix": "na12878_b37_20_21", "Cram2FilteredVcf.info_key": "CNN_2D", "Cram2FilteredVcf.snp_tranches": " --snp-tranche 99.9 ", "Cram2FilteredVcf.indel_tranches": " --indel-tranche 99.5 ", "Cram2FilteredVcf.tensor_type":"read_tensor", - "Cram2FilteredVcf.calling_intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/VQSR/contig20_1m_10m.interval_list", + "Cram2FilteredVcf.calling_intervals": "/home/runner/work/gatk/gatk/src/test/resources/large/VQSR/contig20_1m_10m.interval_list", "Cram2FilteredVcf.gatk_docker": "__GATK_DOCKER__", "Cram2FilteredVcf.preemptible_attempts": 0, "Cram2FilteredVcf.inference_batch_size": 2, diff --git a/scripts/cnv_cromwell_tests/germline/cnv_germline_case_scattered_workflow.json b/scripts/cnv_cromwell_tests/germline/cnv_germline_case_scattered_workflow.json index 3369742b35c..aeb0bb8796d 100644 --- a/scripts/cnv_cromwell_tests/germline/cnv_germline_case_scattered_workflow.json +++ b/scripts/cnv_cromwell_tests/germline/cnv_germline_case_scattered_workflow.json @@ -1,14 +1,14 @@ { "CNVGermlineCaseScatteredWorkflow.normal_bams": [ - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P2T_20xy-downsampled.bam", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P35_20xy-downsampled.bam" + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam", + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P2T_20xy-downsampled.bam", + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P35_20xy-downsampled.bam" ], "CNVGermlineCaseScatteredWorkflow.normal_bais": [ - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam.bai", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P2T_20xy-downsampled.bam.bai", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P35_20xy-downsampled.bam.bai"], - "CNVGermlineCaseScatteredWorkflow.contig_ploidy_model_tar": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wes-do-gc-contig-ploidy-model.tar.gz", + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam.bai", + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P2T_20xy-downsampled.bam.bai", + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P35_20xy-downsampled.bam.bai"], + "CNVGermlineCaseScatteredWorkflow.contig_ploidy_model_tar": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wes-do-gc-contig-ploidy-model.tar.gz", "CNVGermlineCaseScatteredWorkflow.gatk_docker": "__GATK_DOCKER__", "CNVGermlineCaseScatteredWorkflow.allosomal_contigs": ["X", "Y"], "CNVGermlineCaseScatteredWorkflow.ref_copy_number_autosomal_contigs": 2, @@ -17,11 +17,11 @@ "CNVGermlineCaseScatteredWorkflow.gcnv_max_training_epochs": 1, "CNVGermlineCaseScatteredWorkflow.gcnv_min_training_epochs": 1, "CNVGermlineCaseScatteredWorkflow.gcnv_model_tars": [ - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wes-do-gc-gcnv-model-0.tar.gz", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wes-do-gc-gcnv-model-1.tar.gz"], + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wes-do-gc-gcnv-model-0.tar.gz", + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wes-do-gc-gcnv-model-1.tar.gz"], "CNVGermlineCaseScatteredWorkflow.gcnv_num_thermal_advi_iters": 1, - "CNVGermlineCaseScatteredWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/ice_targets_chr20xy.interval_list", - "CNVGermlineCaseScatteredWorkflow.filtered_intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/ice_targets_chr20xy.preprocessed.filtered.interval_list", + "CNVGermlineCaseScatteredWorkflow.intervals": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/ice_targets_chr20xy.interval_list", + "CNVGermlineCaseScatteredWorkflow.filtered_intervals": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/ice_targets_chr20xy.preprocessed.filtered.interval_list", "CNVGermlineCaseScatteredWorkflow.num_intervals_per_scatter": 20, "CNVGermlineCaseScatteredWorkflow.num_samples_per_scatter_block": 2, "CNVGermlineCaseScatteredWorkflow.gcnv_max_advi_iter_first_epoch": 10, @@ -34,7 +34,7 @@ "CNVGermlineCaseScatteredWorkflow.maximum_number_pass_events_per_sample": 10, "CNVGermlineCaseScatteredWorkflow.cpu_for_determine_germline_contig_ploidy": 1, "CNVGermlineCaseScatteredWorkflow.cpu_for_germline_cnv_caller": 1, - "CNVGermlineCaseScatteredWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.dict", - "CNVGermlineCaseScatteredWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta.fai", - "CNVGermlineCaseScatteredWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta" + "CNVGermlineCaseScatteredWorkflow.ref_fasta_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.dict", + "CNVGermlineCaseScatteredWorkflow.ref_fasta_fai": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta.fai", + "CNVGermlineCaseScatteredWorkflow.ref_fasta": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta" } diff --git a/scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_workflow.json b/scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_workflow.json index 6757340df15..0f326877d1d 100644 --- a/scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_workflow.json +++ b/scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_workflow.json @@ -1,6 +1,6 @@ { "CNVGermlineCohortWorkflow.cohort_entity_id": "wes-do-gc", - "CNVGermlineCohortWorkflow.contig_ploidy_priors": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/contig_ploidy_priors_chr20xy.tsv", + "CNVGermlineCohortWorkflow.contig_ploidy_priors": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/contig_ploidy_priors_chr20xy.tsv", "CNVGermlineCohortWorkflow.do_explicit_gc_correction": "true", "CNVGermlineCohortWorkflow.gatk_docker": "__GATK_DOCKER__", "CNVGermlineCohortWorkflow.allosomal_contigs": ["X", "Y"], @@ -10,24 +10,24 @@ "CNVGermlineCohortWorkflow.gcnv_max_training_epochs": 1, "CNVGermlineCohortWorkflow.gcnv_min_training_epochs": 1, "CNVGermlineCohortWorkflow.gcnv_num_thermal_advi_iters": 1, - "CNVGermlineCohortWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/ice_targets_chr20xy.interval_list", + "CNVGermlineCohortWorkflow.intervals": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/ice_targets_chr20xy.interval_list", "CNVGermlineCohortWorkflow.normal_bais": [ - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam.bai", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P2T_20xy-downsampled.bam.bai", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P35_20xy-downsampled.bam.bai"], + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam.bai", + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P2T_20xy-downsampled.bam.bai", + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P35_20xy-downsampled.bam.bai"], "CNVGermlineCohortWorkflow.normal_bams": [ - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P2T_20xy-downsampled.bam", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P35_20xy-downsampled.bam"], + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam", + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P2T_20xy-downsampled.bam", + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P35_20xy-downsampled.bam"], "CNVGermlineCohortWorkflow.num_intervals_per_scatter": 20, "CNVGermlineCohortWorkflow.gcnv_max_copy_number": 3, - "CNVGermlineCohortWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.dict", - "CNVGermlineCohortWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta.fai", - "CNVGermlineCohortWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta", - "CNVGermlineCohortWorkflow.mappability_track_bed": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/umap-k100-single-read-mappability-merged-20xy.bed.gz", - "CNVGermlineCohortWorkflow.mappability_track_bed_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/umap-k100-single-read-mappability-merged-20xy.bed.gz.tbi", - "CNVGermlineCohortWorkflow.segmental_duplication_track_bed": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/segmental-duplication-20xy.bed.gz", - "CNVGermlineCohortWorkflow.segmental_duplication_track_bed_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/segmental-duplication-20xy.bed.gz.tbi", + "CNVGermlineCohortWorkflow.ref_fasta_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.dict", + "CNVGermlineCohortWorkflow.ref_fasta_fai": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta.fai", + "CNVGermlineCohortWorkflow.ref_fasta": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta", + "CNVGermlineCohortWorkflow.mappability_track_bed": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/umap-k100-single-read-mappability-merged-20xy.bed.gz", + "CNVGermlineCohortWorkflow.mappability_track_bed_idx": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/umap-k100-single-read-mappability-merged-20xy.bed.gz.tbi", + "CNVGermlineCohortWorkflow.segmental_duplication_track_bed": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/segmental-duplication-20xy.bed.gz", + "CNVGermlineCohortWorkflow.segmental_duplication_track_bed_idx": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_germline_workflows_test_files/segmental-duplication-20xy.bed.gz.tbi", "CNVGermlineCohortWorkflow.minimum_gc_content": 0.0, "CNVGermlineCohortWorkflow.maximum_gc_content": 1.0, "CNVGermlineCohortWorkflow.minimum_mappability": 0.0, diff --git a/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh b/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh index e31c712330b..97305996d54 100644 --- a/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh +++ b/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh @@ -2,7 +2,7 @@ set -e MODE=$1 -# We split up the test into CASE in COHORT to reduce overall travis runtime +# We split up the test into CASE in COHORT to reduce overall test runtime if [[ "$MODE" != "COHORT" ]] && [[ "$MODE" != "CASE" ]]; then echo "First argument to this scripts needs to be COHORT or CASE" exit 1 @@ -13,20 +13,20 @@ fi script_path=$( cd "$(dirname "${BASH_SOURCE}")" ; pwd -P ) cd "$script_path" -ln -fs /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/cnv_common_tasks.wdl -ln -fs /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl +WORKING_DIR=/home/runner/work/gatk -WORKING_DIR=/home/travis/build/broadinstitute +ln -fs $WORKING_DIR/scripts/cnv_wdl/cnv_common_tasks.wdl +ln -fs $WORKING_DIR/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl pushd . echo "Building docker without running unit tests... =========" cd $WORKING_DIR/gatk # IMPORTANT: This code is duplicated in the M2 WDL test. -if [ ${TRAVIS_PULL_REQUEST} != false ]; then +if [ ! -z "$CI_PULL_REQUEST" ]; then HASH_TO_USE=FETCH_HEAD - sudo bash build_docker.sh -e ${HASH_TO_USE} -s -u -d $PWD/temp_staging/ -t ${TRAVIS_PULL_REQUEST}; + sudo bash build_docker.sh -e ${HASH_TO_USE} -s -u -d $PWD/temp_staging/ -t ${CI_PULL_REQUEST}; else - HASH_TO_USE=${TRAVIS_COMMIT} + HASH_TO_USE=${CI_COMMIT} sudo bash build_docker.sh -e ${HASH_TO_USE} -s -u -d $PWD/temp_staging/; fi echo "Docker build done ==========" @@ -41,10 +41,11 @@ echo "Running ========" # Cohort WES w/ explicit GC correction if [[ "$MODE" == "COHORT" ]]; then - java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl -i cnv_germline_cohort_workflow_mod.json + java -jar ${CROMWELL_JAR} run $WORKING_DIR/gatk/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl -i cnv_germline_cohort_workflow_mod.json ; + find /home/runner/work/gatk/gatk/scripts/cnv_cromwell_tests/germline/cromwell-executions/CNVGermlineCohortWorkflow/ | grep 'stdout\|stderr' | xargs cat ; fi # Scattered case WES w/ explicit GC correction if [[ "$MODE" == "CASE" ]]; then - java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_case_scattered_workflow.wdl -i cnv_germline_case_scattered_workflow_mod.json + java -jar ${CROMWELL_JAR} run $WORKING_DIR/gatk/scripts/cnv_wdl/germline/cnv_germline_case_scattered_workflow.wdl -i cnv_germline_case_scattered_workflow_mod.json fi \ No newline at end of file diff --git a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_do-gc_workflow.json b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_do-gc_workflow.json index 2d03d9d4f08..14de1991bbf 100644 --- a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_do-gc_workflow.json +++ b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_do-gc_workflow.json @@ -1,13 +1,13 @@ { - "CNVSomaticPairWorkflow.common_sites": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/common_snps_sample-chr20.interval_list", + "CNVSomaticPairWorkflow.common_sites": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/common_snps_sample-chr20.interval_list", "CNVSomaticPairWorkflow.gatk_docker": "__GATK_DOCKER__", - "CNVSomaticPairWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/ice_targets_sample-chr20.interval_list", - "CNVSomaticPairWorkflow.normal_bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram", - "CNVSomaticPairWorkflow.normal_bam_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram.crai", - "CNVSomaticPairWorkflow.read_count_pon": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wes-do-gc.pon.hdf5", - "CNVSomaticPairWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", - "CNVSomaticPairWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", - "CNVSomaticPairWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta", - "CNVSomaticPairWorkflow.tumor_bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam", - "CNVSomaticPairWorkflow.tumor_bam_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam.bai" + "CNVSomaticPairWorkflow.intervals": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/ice_targets_sample-chr20.interval_list", + "CNVSomaticPairWorkflow.normal_bam": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram", + "CNVSomaticPairWorkflow.normal_bam_idx": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram.crai", + "CNVSomaticPairWorkflow.read_count_pon": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wes-do-gc.pon.hdf5", + "CNVSomaticPairWorkflow.ref_fasta_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", + "CNVSomaticPairWorkflow.ref_fasta_fai": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", + "CNVSomaticPairWorkflow.ref_fasta": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta", + "CNVSomaticPairWorkflow.tumor_bam": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam", + "CNVSomaticPairWorkflow.tumor_bam_idx": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam.bai" } diff --git a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_do-gc_workflow_funcotator.json b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_do-gc_workflow_funcotator.json index afb8f06d5a5..4ffa8551a32 100644 --- a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_do-gc_workflow_funcotator.json +++ b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_do-gc_workflow_funcotator.json @@ -1,16 +1,16 @@ { - "CNVSomaticPairWorkflow.common_sites": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/common_snps_sample-chr20.interval_list", + "CNVSomaticPairWorkflow.common_sites": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/common_snps_sample-chr20.interval_list", "CNVSomaticPairWorkflow.gatk_docker": "__GATK_DOCKER__", - "CNVSomaticPairWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/ice_targets_sample-chr20.interval_list", + "CNVSomaticPairWorkflow.intervals": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/ice_targets_sample-chr20.interval_list", "CNVSomaticPairWorkflow.is_run_funcotator": "true", "CNVSomaticPairWorkflow.funcotator_is_removing_untared_datasources": "true", - "CNVSomaticPairWorkflow.funcotator_data_sources_tar_gz": "/home/travis/build/broadinstitute/ds.tar.gz", - "CNVSomaticPairWorkflow.normal_bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram", - "CNVSomaticPairWorkflow.normal_bam_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram.crai", - "CNVSomaticPairWorkflow.read_count_pon": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wes-do-gc.pon.hdf5", - "CNVSomaticPairWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", - "CNVSomaticPairWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", - "CNVSomaticPairWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta", - "CNVSomaticPairWorkflow.tumor_bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam", - "CNVSomaticPairWorkflow.tumor_bam_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam.bai" + "CNVSomaticPairWorkflow.funcotator_data_sources_tar_gz": "/home/runner/work/gatk/gatk/ds.tar.gz", + "CNVSomaticPairWorkflow.normal_bam": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram", + "CNVSomaticPairWorkflow.normal_bam_idx": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram.crai", + "CNVSomaticPairWorkflow.read_count_pon": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wes-do-gc.pon.hdf5", + "CNVSomaticPairWorkflow.ref_fasta_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", + "CNVSomaticPairWorkflow.ref_fasta_fai": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", + "CNVSomaticPairWorkflow.ref_fasta": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta", + "CNVSomaticPairWorkflow.tumor_bam": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam", + "CNVSomaticPairWorkflow.tumor_bam_idx": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam.bai" } diff --git a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_no-gc_tumor_only_workflow.json b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_no-gc_tumor_only_workflow.json index 0bef82020ff..dd5bc025f2f 100644 --- a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_no-gc_tumor_only_workflow.json +++ b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_no-gc_tumor_only_workflow.json @@ -1,11 +1,11 @@ { - "CNVSomaticPairWorkflow.common_sites": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/common_snps_sample-chr20.interval_list", + "CNVSomaticPairWorkflow.common_sites": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/common_snps_sample-chr20.interval_list", "CNVSomaticPairWorkflow.gatk_docker": "__GATK_DOCKER__", - "CNVSomaticPairWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/ice_targets_sample-chr20.interval_list", - "CNVSomaticPairWorkflow.read_count_pon": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wes-no-gc.pon.hdf5", - "CNVSomaticPairWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", - "CNVSomaticPairWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", - "CNVSomaticPairWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta", - "CNVSomaticPairWorkflow.tumor_bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam", - "CNVSomaticPairWorkflow.tumor_bam_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam.bai" + "CNVSomaticPairWorkflow.intervals": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/ice_targets_sample-chr20.interval_list", + "CNVSomaticPairWorkflow.read_count_pon": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wes-no-gc.pon.hdf5", + "CNVSomaticPairWorkflow.ref_fasta_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", + "CNVSomaticPairWorkflow.ref_fasta_fai": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", + "CNVSomaticPairWorkflow.ref_fasta": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta", + "CNVSomaticPairWorkflow.tumor_bam": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam", + "CNVSomaticPairWorkflow.tumor_bam_idx": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam.bai" } diff --git a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_no-gc_workflow.json b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_no-gc_workflow.json index 7363bde2d44..8441d46b8fd 100644 --- a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_no-gc_workflow.json +++ b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_no-gc_workflow.json @@ -1,13 +1,13 @@ { - "CNVSomaticPairWorkflow.common_sites": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/common_snps_sample-chr20.interval_list", + "CNVSomaticPairWorkflow.common_sites": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/common_snps_sample-chr20.interval_list", "CNVSomaticPairWorkflow.gatk_docker": "__GATK_DOCKER__", - "CNVSomaticPairWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/ice_targets_sample-chr20.interval_list", - "CNVSomaticPairWorkflow.normal_bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram", - "CNVSomaticPairWorkflow.normal_bam_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram.crai", - "CNVSomaticPairWorkflow.read_count_pon": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wes-no-gc.pon.hdf5", - "CNVSomaticPairWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", - "CNVSomaticPairWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", - "CNVSomaticPairWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta", - "CNVSomaticPairWorkflow.tumor_bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam", - "CNVSomaticPairWorkflow.tumor_bam_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam.bai" + "CNVSomaticPairWorkflow.intervals": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/ice_targets_sample-chr20.interval_list", + "CNVSomaticPairWorkflow.normal_bam": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram", + "CNVSomaticPairWorkflow.normal_bam_idx": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram.crai", + "CNVSomaticPairWorkflow.read_count_pon": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wes-no-gc.pon.hdf5", + "CNVSomaticPairWorkflow.ref_fasta_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", + "CNVSomaticPairWorkflow.ref_fasta_fai": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", + "CNVSomaticPairWorkflow.ref_fasta": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta", + "CNVSomaticPairWorkflow.tumor_bam": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam", + "CNVSomaticPairWorkflow.tumor_bam_idx": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam.bai" } diff --git a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wgs_do-gc_tumor_only_workflow.json b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wgs_do-gc_tumor_only_workflow.json index 793230b2500..313cb37e5f4 100644 --- a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wgs_do-gc_tumor_only_workflow.json +++ b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wgs_do-gc_tumor_only_workflow.json @@ -1,12 +1,12 @@ { - "CNVSomaticPairWorkflow.common_sites": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/common_snps_sample-chr20.interval_list", + "CNVSomaticPairWorkflow.common_sites": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/common_snps_sample-chr20.interval_list", "CNVSomaticPairWorkflow.gatk_docker": "__GATK_DOCKER__", - "CNVSomaticPairWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/chr20.interval_list", + "CNVSomaticPairWorkflow.intervals": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/chr20.interval_list", "CNVSomaticPairWorkflow.bin_length": "10000", - "CNVSomaticPairWorkflow.read_count_pon": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5", - "CNVSomaticPairWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", - "CNVSomaticPairWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", - "CNVSomaticPairWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta", - "CNVSomaticPairWorkflow.tumor_bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam", - "CNVSomaticPairWorkflow.tumor_bam_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam.bai" + "CNVSomaticPairWorkflow.read_count_pon": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5", + "CNVSomaticPairWorkflow.ref_fasta_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", + "CNVSomaticPairWorkflow.ref_fasta_fai": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", + "CNVSomaticPairWorkflow.ref_fasta": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta", + "CNVSomaticPairWorkflow.tumor_bam": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam", + "CNVSomaticPairWorkflow.tumor_bam_idx": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam.bai" } \ No newline at end of file diff --git a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wgs_do-gc_workflow.json b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wgs_do-gc_workflow.json index fb2caed9607..ae971b3dcb7 100644 --- a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wgs_do-gc_workflow.json +++ b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wgs_do-gc_workflow.json @@ -1,14 +1,14 @@ { - "CNVSomaticPairWorkflow.common_sites": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/common_snps_sample-chr20.interval_list", + "CNVSomaticPairWorkflow.common_sites": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/common_snps_sample-chr20.interval_list", "CNVSomaticPairWorkflow.gatk_docker": "__GATK_DOCKER__", - "CNVSomaticPairWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/chr20.interval_list", - "CNVSomaticPairWorkflow.normal_bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143_BL-n1-chr20-downsampled.deduplicated.bam", - "CNVSomaticPairWorkflow.normal_bam_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143_BL-n1-chr20-downsampled.deduplicated.bam.bai", + "CNVSomaticPairWorkflow.intervals": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/chr20.interval_list", + "CNVSomaticPairWorkflow.normal_bam": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143_BL-n1-chr20-downsampled.deduplicated.bam", + "CNVSomaticPairWorkflow.normal_bam_idx": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143_BL-n1-chr20-downsampled.deduplicated.bam.bai", "CNVSomaticPairWorkflow.bin_length": "10000", - "CNVSomaticPairWorkflow.read_count_pon": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5", - "CNVSomaticPairWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", - "CNVSomaticPairWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", - "CNVSomaticPairWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta", - "CNVSomaticPairWorkflow.tumor_bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam", - "CNVSomaticPairWorkflow.tumor_bam_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam.bai" + "CNVSomaticPairWorkflow.read_count_pon": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5", + "CNVSomaticPairWorkflow.ref_fasta_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", + "CNVSomaticPairWorkflow.ref_fasta_fai": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", + "CNVSomaticPairWorkflow.ref_fasta": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta", + "CNVSomaticPairWorkflow.tumor_bam": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam", + "CNVSomaticPairWorkflow.tumor_bam_idx": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam.bai" } \ No newline at end of file diff --git a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wgs_no-gc_workflow.json b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wgs_no-gc_workflow.json index e550fd85349..e2f4412b414 100644 --- a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wgs_no-gc_workflow.json +++ b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wgs_no-gc_workflow.json @@ -1,14 +1,14 @@ { - "CNVSomaticPairWorkflow.common_sites": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/common_snps_sample-chr20.interval_list", + "CNVSomaticPairWorkflow.common_sites": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/common_snps_sample-chr20.interval_list", "CNVSomaticPairWorkflow.gatk_docker": "__GATK_DOCKER__", - "CNVSomaticPairWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/chr20.interval_list", - "CNVSomaticPairWorkflow.normal_bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143_BL-n1-chr20-downsampled.deduplicated.bam", - "CNVSomaticPairWorkflow.normal_bam_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143_BL-n1-chr20-downsampled.deduplicated.bam.bai", + "CNVSomaticPairWorkflow.intervals": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/chr20.interval_list", + "CNVSomaticPairWorkflow.normal_bam": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143_BL-n1-chr20-downsampled.deduplicated.bam", + "CNVSomaticPairWorkflow.normal_bam_idx": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143_BL-n1-chr20-downsampled.deduplicated.bam.bai", "CNVSomaticPairWorkflow.bin_length": "10000", - "CNVSomaticPairWorkflow.read_count_pon": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5", - "CNVSomaticPairWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", - "CNVSomaticPairWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", - "CNVSomaticPairWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta", - "CNVSomaticPairWorkflow.tumor_bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam", - "CNVSomaticPairWorkflow.tumor_bam_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam.bai" + "CNVSomaticPairWorkflow.read_count_pon": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5", + "CNVSomaticPairWorkflow.ref_fasta_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", + "CNVSomaticPairWorkflow.ref_fasta_fai": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", + "CNVSomaticPairWorkflow.ref_fasta": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta", + "CNVSomaticPairWorkflow.tumor_bam": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam", + "CNVSomaticPairWorkflow.tumor_bam_idx": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam.bai" } \ No newline at end of file diff --git a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wes_do-gc_workflow.json b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wes_do-gc_workflow.json index 7e13604400b..8c8bd7a0679 100644 --- a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wes_do-gc_workflow.json +++ b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wes_do-gc_workflow.json @@ -1,15 +1,15 @@ { "CNVSomaticPanelWorkflow.do_explicit_gc_correction": "true", "CNVSomaticPanelWorkflow.gatk_docker": "__GATK_DOCKER__", - "CNVSomaticPanelWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/ice_targets_sample-chr20.interval_list", + "CNVSomaticPanelWorkflow.intervals": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/ice_targets_sample-chr20.interval_list", "CNVSomaticPanelWorkflow.normal_bais": [ - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram.crai", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam.bai"], + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram.crai", + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam.bai"], "CNVSomaticPanelWorkflow.normal_bams": [ - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam"], + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram", + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam"], "CNVSomaticPanelWorkflow.pon_entity_id": "wes-do-gc", - "CNVSomaticPanelWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", - "CNVSomaticPanelWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", - "CNVSomaticPanelWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta" + "CNVSomaticPanelWorkflow.ref_fasta_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", + "CNVSomaticPanelWorkflow.ref_fasta_fai": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", + "CNVSomaticPanelWorkflow.ref_fasta": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta" } diff --git a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wes_no-gc_workflow.json b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wes_no-gc_workflow.json index 3d77533a87d..ad7c7f4be06 100644 --- a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wes_no-gc_workflow.json +++ b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wes_no-gc_workflow.json @@ -1,14 +1,14 @@ { "CNVSomaticPanelWorkflow.gatk_docker": "__GATK_DOCKER__", - "CNVSomaticPanelWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/ice_targets_sample-chr20.interval_list", + "CNVSomaticPanelWorkflow.intervals": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/ice_targets_sample-chr20.interval_list", "CNVSomaticPanelWorkflow.normal_bais": [ - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram.crai", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam.bai"], + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram.crai", + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam.bai"], "CNVSomaticPanelWorkflow.normal_bams": [ - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam"], + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram", + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam"], "CNVSomaticPanelWorkflow.pon_entity_id": "wes-no-gc", - "CNVSomaticPanelWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", - "CNVSomaticPanelWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", - "CNVSomaticPanelWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta" + "CNVSomaticPanelWorkflow.ref_fasta_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", + "CNVSomaticPanelWorkflow.ref_fasta_fai": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", + "CNVSomaticPanelWorkflow.ref_fasta": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta" } \ No newline at end of file diff --git a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wgs_do-gc_workflow.json b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wgs_do-gc_workflow.json index 42f199479de..2e0d653d719 100644 --- a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wgs_do-gc_workflow.json +++ b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wgs_do-gc_workflow.json @@ -1,16 +1,16 @@ { "CNVSomaticPanelWorkflow.do_explicit_gc_correction": "true", "CNVSomaticPanelWorkflow.gatk_docker": "__GATK_DOCKER__", - "CNVSomaticPanelWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/chr20.interval_list", + "CNVSomaticPanelWorkflow.intervals": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/chr20.interval_list", "CNVSomaticPanelWorkflow.normal_bais": [ - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143_BL-n1-chr20-downsampled.deduplicated.bam.bai", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam.bai"], + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143_BL-n1-chr20-downsampled.deduplicated.bam.bai", + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam.bai"], "CNVSomaticPanelWorkflow.normal_bams": [ - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143_BL-n1-chr20-downsampled.deduplicated.bam", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam"], + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143_BL-n1-chr20-downsampled.deduplicated.bam", + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam"], "CNVSomaticPanelWorkflow.pon_entity_id": "wgs-do-gc", "CNVSomaticPanelWorkflow.bin_length": "10000", - "CNVSomaticPanelWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", - "CNVSomaticPanelWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", - "CNVSomaticPanelWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta" + "CNVSomaticPanelWorkflow.ref_fasta_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", + "CNVSomaticPanelWorkflow.ref_fasta_fai": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", + "CNVSomaticPanelWorkflow.ref_fasta": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta" } diff --git a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wgs_no-gc_workflow.json b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wgs_no-gc_workflow.json index f200a65198c..a61586b3ca2 100644 --- a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wgs_no-gc_workflow.json +++ b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wgs_no-gc_workflow.json @@ -1,15 +1,15 @@ { "CNVSomaticPanelWorkflow.gatk_docker": "__GATK_DOCKER__", - "CNVSomaticPanelWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/chr20.interval_list", + "CNVSomaticPanelWorkflow.intervals": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/chr20.interval_list", "CNVSomaticPanelWorkflow.normal_bais": [ - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143_BL-n1-chr20-downsampled.deduplicated.bam.bai", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam.bai"], + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143_BL-n1-chr20-downsampled.deduplicated.bam.bai", + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam.bai"], "CNVSomaticPanelWorkflow.normal_bams": [ - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143_BL-n1-chr20-downsampled.deduplicated.bam", - "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam"], + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143_BL-n1-chr20-downsampled.deduplicated.bam", + "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam"], "CNVSomaticPanelWorkflow.pon_entity_id": "wgs-no-gc", "CNVSomaticPanelWorkflow.bin_length": "10000", - "CNVSomaticPanelWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", - "CNVSomaticPanelWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", - "CNVSomaticPanelWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta" + "CNVSomaticPanelWorkflow.ref_fasta_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict", + "CNVSomaticPanelWorkflow.ref_fasta_fai": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai", + "CNVSomaticPanelWorkflow.ref_fasta": "/home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta" } diff --git a/scripts/cnv_cromwell_tests/somatic/run_cnv_somatic_workflows.sh b/scripts/cnv_cromwell_tests/somatic/run_cnv_somatic_workflows.sh index ecd376f26df..30c16b6cb97 100644 --- a/scripts/cnv_cromwell_tests/somatic/run_cnv_somatic_workflows.sh +++ b/scripts/cnv_cromwell_tests/somatic/run_cnv_somatic_workflows.sh @@ -4,20 +4,20 @@ set -e script_path=$( cd "$(dirname "${BASH_SOURCE}")" ; pwd -P ) cd "$script_path" -ln -fs /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/cnv_common_tasks.wdl -ln -fs /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/somatic/cnv_somatic_oncotator_workflow.wdl +WORKING_DIR=/home/runner/work/gatk -WORKING_DIR=/home/travis/build/broadinstitute +ln -fs $WORKING_DIR/scripts/cnv_wdl/cnv_common_tasks.wdl +ln -fs $WORKING_DIR/scripts/cnv_wdl/somatic/cnv_somatic_oncotator_workflow.wdl pushd . echo "Building docker without running unit tests... =========" cd $WORKING_DIR/gatk # IMPORTANT: This code is duplicated in the M2 WDL test. -if [ ${TRAVIS_PULL_REQUEST} != false ]; then +if [ ! -z "$CI_PULL_REQUEST" ]; then HASH_TO_USE=FETCH_HEAD - sudo bash build_docker.sh -e ${HASH_TO_USE} -s -u -d $PWD/temp_staging/ -t ${TRAVIS_PULL_REQUEST}; + sudo bash build_docker.sh -e ${HASH_TO_USE} -s -u -d $PWD/temp_staging/ -t ${CI_PULL_REQUEST}; else - HASH_TO_USE=${TRAVIS_COMMIT} + HASH_TO_USE=${CI_COMMIT} sudo bash build_docker.sh -e ${HASH_TO_USE} -s -u -d $PWD/temp_staging/; fi echo "Docker build done ==========" @@ -42,36 +42,36 @@ sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" ${CNV_CROMWELL_T echo "Running ========" # Panel WES -java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl -i cnv_somatic_panel_wes_no-gc_workflow_mod.json +java -jar ${CROMWELL_JAR} run $WORKING_DIR/gatk/scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl -i cnv_somatic_panel_wes_no-gc_workflow_mod.json # Panel WGS -java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl -i cnv_somatic_panel_wgs_no-gc_workflow_mod.json +java -jar ${CROMWELL_JAR} run $WORKING_DIR/gatk/scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl -i cnv_somatic_panel_wgs_no-gc_workflow_mod.json # Panel WES w/ explicit GC correction -java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl -i cnv_somatic_panel_wes_do-gc_workflow_mod.json +java -jar ${CROMWELL_JAR} run $WORKING_DIR/gatk/scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl -i cnv_somatic_panel_wes_do-gc_workflow_mod.json # Panel WGS w/ explicit GC correction -java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl -i cnv_somatic_panel_wgs_do-gc_workflow_mod.json +java -jar ${CROMWELL_JAR} run $WORKING_DIR/gatk/scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl -i cnv_somatic_panel_wgs_do-gc_workflow_mod.json # Pair WES -java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl -i cnv_somatic_pair_wes_no-gc_workflow_mod.json +java -jar ${CROMWELL_JAR} run $WORKING_DIR/gatk/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl -i cnv_somatic_pair_wes_no-gc_workflow_mod.json # Pair WGS -java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl -i cnv_somatic_pair_wgs_no-gc_workflow_mod.json +java -jar ${CROMWELL_JAR} run $WORKING_DIR/gatk/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl -i cnv_somatic_pair_wgs_no-gc_workflow_mod.json # Pair WES w/ explicit GC correction -java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl -i cnv_somatic_pair_wes_do-gc_workflow_mod.json +java -jar ${CROMWELL_JAR} run $WORKING_DIR/gatk/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl -i cnv_somatic_pair_wes_do-gc_workflow_mod.json # Pair WGS w/ explicit GC correction -java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl -i cnv_somatic_pair_wgs_do-gc_workflow_mod.json +java -jar ${CROMWELL_JAR} run $WORKING_DIR/gatk/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl -i cnv_somatic_pair_wgs_do-gc_workflow_mod.json # Tumor only WGS w/ explicit GC correction -java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl -i cnv_somatic_pair_wgs_do-gc_tumor_only_workflow_mod.json +java -jar ${CROMWELL_JAR} run $WORKING_DIR/gatk/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl -i cnv_somatic_pair_wgs_do-gc_tumor_only_workflow_mod.json # Tumor only WES w/o explicit GC correction -java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl -i cnv_somatic_pair_wes_no-gc_tumor_only_workflow_mod.json +java -jar ${CROMWELL_JAR} run $WORKING_DIR/gatk/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl -i cnv_somatic_pair_wes_no-gc_tumor_only_workflow_mod.json #### Test FuncotateSegments on a small run. # Must tar up test datasources for the WDL echo "Preparing small gencode-only datasource dir for funcotator test..." pushd . -cd /home/travis/build/broadinstitute/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/ -tar zcvf /home/travis/build/broadinstitute/ds.tar.gz small_cntn4_ds/gencode_cntn4/ +cd $WORKING_DIR/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/ +tar zcvf $WORKING_DIR/gatk/ds.tar.gz small_cntn4_ds/gencode_cntn4/ popd # Pair WES with funcotator -java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl \ +java -jar ${CROMWELL_JAR} run $WORKING_DIR/gatk/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl \ -i cnv_somatic_pair_wes_do-gc_workflow_funcotator_mod.json ##### diff --git a/scripts/github_actions/README.md b/scripts/github_actions/README.md new file mode 100644 index 00000000000..e6d1ba282b3 --- /dev/null +++ b/scripts/github_actions/README.md @@ -0,0 +1 @@ +These scripts are intended to be run on github-actions CI and may not run correctly outside of that environment. \ No newline at end of file diff --git a/scripts/travis/Reporter.py b/scripts/github_actions/Reporter.py similarity index 72% rename from scripts/travis/Reporter.py rename to scripts/github_actions/Reporter.py index d370745cb00..4e939080393 100644 --- a/scripts/travis/Reporter.py +++ b/scripts/github_actions/Reporter.py @@ -2,7 +2,7 @@ # # This script creates a comment on github using the API token provided through GITHUB_API_TOKEN # It first checks if a comment already exists which was made with the given identity -# and which mentions the same travis build ID as the current running one in the first line of the comment. +# and which mentions the same github actions build ID as the current running one in the first line of the comment. # If no comment is found it creates a new one with a header and the log url. # If a matching comment is found this appends it's log information to the existing comment. # @@ -14,22 +14,21 @@ from github import Github -key = os.environ["GITHUB_API_TOKEN"] +key = os.environ["GITHUB_TOKEN"] test_type = os.getenv("TEST_TYPE", "") g = Github(key) github_login = g.get_user().login -pull_number = os.environ["TRAVIS_PULL_REQUEST"] -repo_name = os.environ["TRAVIS_REPO_SLUG"] -job_number = os.environ["TRAVIS_JOB_NUMBER"] -job_id = os.environ["TRAVIS_JOB_ID"] -build_number = os.environ["TRAVIS_BUILD_NUMBER"] -build_id = os.environ["TRAVIS_BUILD_ID"] -jdk_version = os.getenv("TRAVIS_JDK_VERSION","") -travis_page_url = os.getenv("TRAVIS_BUILD_WEB_URL") -job_page_url = os.getenv("TRAVIS_JOB_WEB_URL") +pull_number = os.environ["GITHUB_EVENT_NUMBER"] +repo_name = os.environ["GITHUB_REPOSITORY"] +job_number = os.environ["JOB_MATRIX_ID"] +job_id = os.environ["GITHUB_RUN_ID"] +build_id = os.environ["GITHUB_RUN_ID"] +jdk_version = os.getenv("JDK_VERSION","") +job_page_url = os.getenv("GITHUB_LOGS_URL") +workflow_url = os.getenv("ACTIONS_JOB_WEB_URL") repo = g.get_repo(repo_name) pull = repo.get_pull(int(pull_number)) @@ -54,7 +53,7 @@ def update(comment): def new_comment(pull): - pull.create_issue_comment("Travis reported job failures from build [%s](%s)" % (build_number, travis_page_url) + pull.create_issue_comment("Github actions tests reported job failures from actions build [%s](%s)" % (build_id, workflow_url) + "\nFailures in the following jobs:" + "\n" + "\n | Test Type | JDK | Job ID | Logs |" diff --git a/scripts/m2_cromwell_tests/pair_list b/scripts/m2_cromwell_tests/pair_list index 688cab6af35..962fe49cca2 100644 --- a/scripts/m2_cromwell_tests/pair_list +++ b/scripts/m2_cromwell_tests/pair_list @@ -1,2 +1,2 @@ -/home/travis/build/broadinstitute/gatk/src/test/resources/large/mutect/dream_synthetic_bams/tumor_1.bam /home/travis/build/broadinstitute/gatk/src/test/resources/large/mutect/dream_synthetic_bams/tumor_1.bam.bai /home/travis/build/broadinstitute/gatk/src/test/resources/large/mutect/dream_synthetic_bams/normal_1.bam /home/travis/build/broadinstitute/gatk/src/test/resources/large/mutect/dream_synthetic_bams/normal_1.bam.bai -/home/travis/build/broadinstitute/gatk/src/test/resources/large/mutect/dream_synthetic_bams/tumor_2.bam /home/travis/build/broadinstitute/gatk/src/test/resources/large/mutect/dream_synthetic_bams/tumor_2.bam.bai /home/travis/build/broadinstitute/gatk/src/test/resources/large/mutect/dream_synthetic_bams/normal_2.bam /home/travis/build/broadinstitute/gatk/src/test/resources/large/mutect/dream_synthetic_bams/normal_2.bam.bai +/home/runner/work/gatk/gatk/src/test/resources/large/mutect/dream_synthetic_bams/tumor_1.bam /home/runner/work/gatk/gatk/src/test/resources/large/mutect/dream_synthetic_bams/tumor_1.bam.bai /home/runner/work/gatk/gatk/src/test/resources/large/mutect/dream_synthetic_bams/normal_1.bam /home/runner/work/gatk/gatk/src/test/resources/large/mutect/dream_synthetic_bams/normal_1.bam.bai +/home/runner/work/gatk/gatk/src/test/resources/large/mutect/dream_synthetic_bams/tumor_2.bam /home/runner/work/gatk/gatk/src/test/resources/large/mutect/dream_synthetic_bams/tumor_2.bam.bai /home/runner/work/gatk/gatk/src/test/resources/large/mutect/dream_synthetic_bams/normal_2.bam /home/runner/work/gatk/gatk/src/test/resources/large/mutect/dream_synthetic_bams/normal_2.bam.bai diff --git a/scripts/m2_cromwell_tests/pair_list_tumor_only b/scripts/m2_cromwell_tests/pair_list_tumor_only index 812bd83ffb8..9498e7e342f 100644 --- a/scripts/m2_cromwell_tests/pair_list_tumor_only +++ b/scripts/m2_cromwell_tests/pair_list_tumor_only @@ -1,2 +1,2 @@ -/home/travis/build/broadinstitute/gatk/src/test/resources/large/mutect/dream_synthetic_bams/tumor_1.bam /home/travis/build/broadinstitute/gatk/src/test/resources/large/mutect/dream_synthetic_bams/tumor_1.bam.bai -/home/travis/build/broadinstitute/gatk/src/test/resources/large/mutect/dream_synthetic_bams/tumor_2.bam /home/travis/build/broadinstitute/gatk/src/test/resources/large/mutect/dream_synthetic_bams/tumor_2.bam.bai \ No newline at end of file +/home/runner/work/gatk/gatk/src/test/resources/large/mutect/dream_synthetic_bams/tumor_1.bam /home/runner/work/gatk/gatk/src/test/resources/large/mutect/dream_synthetic_bams/tumor_1.bam.bai +/home/runner/work/gatk/gatk/src/test/resources/large/mutect/dream_synthetic_bams/tumor_2.bam /home/runner/work/gatk/gatk/src/test/resources/large/mutect/dream_synthetic_bams/tumor_2.bam.bai \ No newline at end of file diff --git a/scripts/m2_cromwell_tests/run_m2_wdl.sh b/scripts/m2_cromwell_tests/run_m2_wdl.sh index f30f28dfcf9..f7f863e765b 100644 --- a/scripts/m2_cromwell_tests/run_m2_wdl.sh +++ b/scripts/m2_cromwell_tests/run_m2_wdl.sh @@ -4,7 +4,7 @@ set -e script_path=$( cd "$(dirname "${BASH_SOURCE}")" ; pwd -P ) cd "$script_path" -WORKING_DIR=/home/travis/build/broadinstitute +WORKING_DIR=/home/runner/work/gatk set -e @@ -13,7 +13,7 @@ pushd . FUNCOTATOR_TEST_DS_DIR=${WORKING_DIR}/gatk/src/test/resources/large/funcotator/ cd ${FUNCOTATOR_TEST_DS_DIR} # First parameter must match Mutect2_Multi.funco_data_sources_tar_gz test_m2_wdl_multi.json -tar zcvf ${WORKING_DIR}/small_ds_pik3ca.tar.gz small_ds_pik3ca/* +tar zcvf ${WORKING_DIR}/gatk/small_ds_pik3ca.tar.gz small_ds_pik3ca/* popd echo "Building docker image for M2 WDL tests (skipping unit tests)..." @@ -23,11 +23,13 @@ echo "Building docker image for M2 WDL tests (skipping unit tests)..." echo "Building docker without running unit tests... =========" cd $WORKING_DIR/gatk # IMPORTANT: This code is duplicated in the cnv WDL test. -if [ ${TRAVIS_PULL_REQUEST} != false ]; then +if [ ! -z "$CI_PULL_REQUEST" ]; then HASH_TO_USE=FETCH_HEAD - sudo bash build_docker.sh -e ${HASH_TO_USE} -s -u -d $PWD/temp_staging/ -t ${TRAVIS_PULL_REQUEST}; + echo "Building pr build with $HASH_TO_USE... =========" + sudo bash build_docker.sh -e ${HASH_TO_USE} -s -u -d $PWD/temp_staging/ -t ${CI_PULL_REQUEST}; else - HASH_TO_USE=${TRAVIS_COMMIT} + HASH_TO_USE=${CI_COMMIT} + echo "Building commit build with $HASH_TO_USE... =========" sudo bash build_docker.sh -e ${HASH_TO_USE} -s -u -d $PWD/temp_staging/; fi echo "Docker build done ==========" diff --git a/scripts/m2_cromwell_tests/test_m2_wdl_multi.json b/scripts/m2_cromwell_tests/test_m2_wdl_multi.json index c2ea7596cd6..d81b0852158 100644 --- a/scripts/m2_cromwell_tests/test_m2_wdl_multi.json +++ b/scripts/m2_cromwell_tests/test_m2_wdl_multi.json @@ -1,11 +1,11 @@ { "Mutect2_Multi.gatk_docker": "__GATK_DOCKER__", - "Mutect2_Multi.intervals": "/home/travis/build/broadinstitute/gatk/scripts/m2_cromwell_tests/interval_list.interval_list", - "Mutect2_Multi.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta", - "Mutect2_Multi.ref_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta.fai", - "Mutect2_Multi.ref_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/human_g1k_v37.20.21.dict", - "Mutect2_Multi.pair_list": "/home/travis/build/broadinstitute/gatk/scripts/m2_cromwell_tests/pair_list", - "Mutect2_Multi.funco_data_sources_tar_gz": "/home/travis/build/broadinstitute/small_ds_pik3ca.tar.gz", + "Mutect2_Multi.intervals": "/home/runner/work/gatk/gatk/scripts/m2_cromwell_tests/interval_list.interval_list", + "Mutect2_Multi.ref_fasta": "/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta", + "Mutect2_Multi.ref_fai": "/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta.fai", + "Mutect2_Multi.ref_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.dict", + "Mutect2_Multi.pair_list": "/home/runner/work/gatk/gatk/scripts/m2_cromwell_tests/pair_list", + "Mutect2_Multi.funco_data_sources_tar_gz": "/home/runner/work/gatk/gatk/small_ds_pik3ca.tar.gz", "Mutect2_Multi.funco_reference_version": "hg19", "Mutect2_Multi.scatter_count": 2, "Mutect2_Multi.run_orientation_bias_mixture_model_filter": true, diff --git a/scripts/m2_cromwell_tests/test_mitochondria_m2_wdl.json b/scripts/m2_cromwell_tests/test_mitochondria_m2_wdl.json index 51fee139813..a849848bd76 100644 --- a/scripts/m2_cromwell_tests/test_mitochondria_m2_wdl.json +++ b/scripts/m2_cromwell_tests/test_mitochondria_m2_wdl.json @@ -1,27 +1,27 @@ { "MitochondriaPipeline.gatk_docker_override": "__GATK_DOCKER__", - "MitochondriaPipeline.wgs_aligned_input_bam_or_cram": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/NA12878.alignedHg38.duplicateMarked.baseRealigned.bam", - "MitochondriaPipeline.wgs_aligned_input_bam_or_cram_index": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/NA12878.alignedHg38.duplicateMarked.baseRealigned.bam.bai", + "MitochondriaPipeline.wgs_aligned_input_bam_or_cram": "/home/runner/work/gatk/gatk/src/test/resources/large/NA12878.alignedHg38.duplicateMarked.baseRealigned.bam", + "MitochondriaPipeline.wgs_aligned_input_bam_or_cram_index": "/home/runner/work/gatk/gatk/src/test/resources/large/NA12878.alignedHg38.duplicateMarked.baseRealigned.bam.bai", "MitochondriaPipeline.autosomal_coverage": 30, - "MitochondriaPipeline.mt_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.dict", - "MitochondriaPipeline.mt_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.fasta", - "MitochondriaPipeline.mt_fasta_index": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.fasta.fai", - "MitochondriaPipeline.mt_amb": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.fasta.amb", - "MitochondriaPipeline.mt_ann": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.fasta.ann", - "MitochondriaPipeline.mt_bwt": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.fasta.bwt", - "MitochondriaPipeline.mt_pac": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.fasta.pac", - "MitochondriaPipeline.mt_sa": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.fasta.sa", - "MitochondriaPipeline.blacklisted_sites": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/blacklist_sites.hg38.chrM.bed", - "MitochondriaPipeline.blacklisted_sites_index": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/blacklist_sites.hg38.chrM.bed.idx", - "MitochondriaPipeline.mt_shifted_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.dict", - "MitochondriaPipeline.mt_shifted_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta", - "MitochondriaPipeline.mt_shifted_fasta_index": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.fai", - "MitochondriaPipeline.mt_shifted_amb": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.amb", - "MitochondriaPipeline.mt_shifted_ann": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.ann", - "MitochondriaPipeline.mt_shifted_bwt": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.bwt", - "MitochondriaPipeline.mt_shifted_pac": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.pac", - "MitochondriaPipeline.mt_shifted_sa": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.sa", - "MitochondriaPipeline.shift_back_chain": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/ShiftBack.chain", - "MitochondriaPipeline.control_region_shifted_reference_interval_list": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/control_region_shifted.chrM.interval_list", - "MitochondriaPipeline.non_control_region_interval_list": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/mitochondria_references/non_control_region.chrM.interval_list" + "MitochondriaPipeline.mt_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.dict", + "MitochondriaPipeline.mt_fasta": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.fasta", + "MitochondriaPipeline.mt_fasta_index": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.fasta.fai", + "MitochondriaPipeline.mt_amb": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.fasta.amb", + "MitochondriaPipeline.mt_ann": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.fasta.ann", + "MitochondriaPipeline.mt_bwt": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.fasta.bwt", + "MitochondriaPipeline.mt_pac": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.fasta.pac", + "MitochondriaPipeline.mt_sa": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.fasta.sa", + "MitochondriaPipeline.blacklisted_sites": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/blacklist_sites.hg38.chrM.bed", + "MitochondriaPipeline.blacklisted_sites_index": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/blacklist_sites.hg38.chrM.bed.idx", + "MitochondriaPipeline.mt_shifted_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.dict", + "MitochondriaPipeline.mt_shifted_fasta": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta", + "MitochondriaPipeline.mt_shifted_fasta_index": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.fai", + "MitochondriaPipeline.mt_shifted_amb": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.amb", + "MitochondriaPipeline.mt_shifted_ann": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.ann", + "MitochondriaPipeline.mt_shifted_bwt": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.bwt", + "MitochondriaPipeline.mt_shifted_pac": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.pac", + "MitochondriaPipeline.mt_shifted_sa": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.sa", + "MitochondriaPipeline.shift_back_chain": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/ShiftBack.chain", + "MitochondriaPipeline.control_region_shifted_reference_interval_list": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/control_region_shifted.chrM.interval_list", + "MitochondriaPipeline.non_control_region_interval_list": "/home/runner/work/gatk/gatk/src/test/resources/large/mitochondria_references/non_control_region.chrM.interval_list" } diff --git a/scripts/travis/README.md b/scripts/travis/README.md deleted file mode 100644 index fea17270f76..00000000000 --- a/scripts/travis/README.md +++ /dev/null @@ -1 +0,0 @@ -These scripts are intended to be run on Travis CI and may not run correctly outside of that environment. \ No newline at end of file diff --git a/scripts/travis/check_for_pull_request b/scripts/travis/check_for_pull_request deleted file mode 100755 index f7e4b4140eb..00000000000 --- a/scripts/travis/check_for_pull_request +++ /dev/null @@ -1,4 +0,0 @@ -#!/usr/bin/env bash - -#query github for information about a specific pull request -curl -v -H "Authorization: token $GITHUB_API_TOKEN" https://api.github.com/repos/broadinstitute/gatk/pulls\?state\=open\&head="broadinstitute:${TRAVIS_BRANCH}" diff --git a/scripts/travis/install_and_authenticate_to_gcloud.sh b/scripts/travis/install_and_authenticate_to_gcloud.sh deleted file mode 100755 index edc2c48fb3f..00000000000 --- a/scripts/travis/install_and_authenticate_to_gcloud.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env bash -# Install and Gcloud and authenticate on travis. -# This is expected to be run from the travis root directory. - -export BOTO_CONFIG=/dev/null; # see for more information https://github.com/broadinstitute/gatk/pull/3350 -openssl aes-256-cbc -K $encrypted_c51214b7dd65_key -iv $encrypted_c51214b7dd65_iv -in resources_for_CI/servicekey.json.enc -out servicekey.json -d; -scripts/travis/install_gcloud.sh; -$GCLOUD_HOME/gcloud components update --quiet; -if [[ $TEST_TYPE == cloud ]]; then - $GCLOUD_HOME/gcloud components install beta --quiet; -fi; -$GCLOUD_HOME/gcloud config set project broad-dsde-dev; -$GCLOUD_HOME/gcloud auth activate-service-account --key-file servicekey.json; -$GCLOUD_HOME/gcloud --version diff --git a/scripts/travis/install_gcloud.sh b/scripts/travis/install_gcloud.sh deleted file mode 100755 index b62c666d894..00000000000 --- a/scripts/travis/install_gcloud.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/bash -#Install gcloud -if [ ! -d $HOME/gcloud/google-cloud-sdk ]; then - mkdir -p $HOME/gcloud && - wget https://dl.google.com/dl/cloudsdk/release/google-cloud-sdk.tar.gz --directory-prefix=$HOME/gcloud && - cd $HOME/gcloud && - tar xzf google-cloud-sdk.tar.gz && - ./google-cloud-sdk/install.sh --quiet --path-update true && - cd $TRAVIS_BUILD_DIR; -fi