removing remaining travis infrastrucutre and updating some wdl test p…

…aths

.github/actions/upload-results/action.yml

@@ -41,9 +41,12 @@ runs:
         path: build/reports/tests
 
     - name: Upload Reports
+      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 }}/;
-        echo "See the test report at https://storage.googleapis.com${{ env.HELLBENDER_TEST_LOGS }}${{ inputs.repo-path }}/tests/test/index.html";
+        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
@@ -68,7 +71,7 @@ runs:
         echo ${html_url}
       shell: bash
 
-    - name: Updating the PR travis results
+    - name: Updating the PR with failed results
       if: ${{ inputs.warnPR == 'true' }}
       env:
         GITHUB_TOKEN: ${{ inputs.bot-comment-key }}
@@ -82,5 +85,5 @@ runs:
         GITHUB_LOGS_URL: ${{ steps.loghtml.outputs.html_url }}
       run: |
         pip install --user PyGithub;
-        python scripts/github_actions/Reporter.py https://storage.googleapis.com${{ env.HELLBENDER_TEST_LOGS }}${{ inputs.repo-path }}/tests/test/index.html;
+        python scripts/github_actions/Reporter.py ${{ steps.uploadreports.outputs.view_url }};
       shell: bash

.github/workflows/gatk-tests.yml

@@ -47,6 +47,7 @@ jobs:
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
 
+#Run our non-docker tests
   test:
     runs-on: ubuntu-latest
     strategy:
@@ -109,13 +110,14 @@ jobs:
         run: ./gradlew compileTestJava
 
       - name: run-tests
+        id: jacoco-tests
         run: |
           ./gradlew -Dscala.version=${{ env.SCALA_VERSION }} test jacocoTestReport
 
       - uses: /broadinstitute/gatk/.github/actions/upload-results@lb_github_actions
         if: always()
         with:
-          warnPR: ${{ github.event_name == 'pull_request' && steps.run-docker-tests.outcome != 'success' }}
+          warnPR: ${{ github.event_name == 'pull_request' && steps.jacoco-tests.outcome != 'success' }}
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           jdk-version: ${{ matrix.Java }}
           test-type: ${{ matrix.testType }}
@@ -186,6 +188,7 @@ jobs:
         run: git lfs pull
 
       - name: run-docker-tests
+        id: docker-jacocco-tests
         run: |
           docker run \
             -v $(pwd):/gatkCloneMountPoint:cached \
@@ -206,7 +209,7 @@ jobs:
       - uses: /broadinstitute/gatk/.github/actions/upload-results@lb_github_actions
         if: always()
         with:
-          warnPR: ${{ github.event_name == 'pull_request' && steps.run-docker-tests.outcome != 'success' }}
+          warnPR: ${{ github.event_name == 'pull_request' && steps.docker-jacocco-tests.outcome != 'success' }}
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           jdk-version: ${{ matrix.Java }}
           test-type: docker ${{ matrix.testType }}
@@ -266,9 +269,9 @@ jobs:
         run: |
           if [[ "${{ github.event_name }}" == "pull_request" ]]
           then
-            echo "TRAVIS_PULL_REQUEST=${{ github.event.number }}" >> $GITHUB_ENV 
+            echo "CI_PULL_REQUEST=${{ github.event.number }}" >> $GITHUB_ENV 
           fi
-          echo "TRAVIS_COMMIT=${{ github.sha }}" >> $GITHUB_ENV
+          echo "CI_COMMIT=${{ github.sha }}" >> $GITHUB_ENV
 
       - name: "Installing GATK for tests"
         run: |

scripts/cnn_variant_cromwell_tests/run_cnn_variant_wdl.sh

@@ -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 [ ! -z "$TRAVIS_PULL_REQUEST" ]; then
+if [ ! -z "$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

scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh

@@ -22,11 +22,11 @@ pushd .
 echo "Building docker without running unit tests... ========="
 cd $WORKING_DIR/gatk
 # IMPORTANT: This code is duplicated in the M2 WDL test.
-if  [ ! -z "$TRAVIS_PULL_REQUEST" ]; 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 =========="

scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_do-gc_workflow_funcotator.json

@@ -4,7 +4,7 @@
   "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.funcotator_data_sources_tar_gz": "/home/runner/work/gatk/gatk/build/broadinstitute/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",

scripts/cnv_cromwell_tests/somatic/run_cnv_somatic_workflows.sh

@@ -13,11 +13,11 @@ pushd .
 echo "Building docker without running unit tests... ========="
 cd $WORKING_DIR/gatk
 # IMPORTANT: This code is duplicated in the M2 WDL test.
-if [ ! -z "$TRAVIS_PULL_REQUEST" ]; 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 =========="
@@ -68,7 +68,7 @@ java -jar ${CROMWELL_JAR} run $WORKING_DIR/gatk/scripts/cnv_wdl/somatic/cnv_soma
 echo "Preparing small gencode-only datasource dir for funcotator test..."
 pushd .
 cd $WORKING_DIR/gatk/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/
-tar zcvf $WORKING_DIR/build/broadinstitute/ds.tar.gz small_cntn4_ds/gencode_cntn4/
+tar zcvf $WORKING_DIR/gatk/build/broadinstitute/ds.tar.gz small_cntn4_ds/gencode_cntn4/
 popd
 
 # Pair WES with funcotator

scripts/github_actions/README.md

@@ -1 +1 @@
-These scripts are intended to be run on Travis CI and may not run correctly outside of that environment.
+These scripts are intended to be run on github-actions CI and may not run correctly outside of that environment.

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.
 #