diff --git a/.github/actions/install-cromwell/action.yml b/.github/actions/install-cromwell/action.yml
new file mode 100644
index 00000000000..16c237d3079
--- /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'
+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 -O $CROMWELL_JAR https://github.com/broadinstitute/cromwell/releases/download/${{ inputs.CROMWELL_VERSION }}/cromwell-${{ inputs.CROMWELL_VERSION }}.jar;
+        wget -O $WOMTOOL_JAR https://github.com/broadinstitute/cromwell/releases/download/${{ inputs.CROMWELL_VERSION }}/womtool-${{ inputs.CROMWELL_VERSION }}.jar;
+      shell: bash
\ No newline at end of file
diff --git a/.github/actions/upload-results/action.yml b/.github/actions/upload-results/action.yml
new file mode 100644
index 00000000000..2c44aff8fdf
--- /dev/null
+++ b/.github/actions/upload-results/action.yml
@@ -0,0 +1,89 @@
+name: 'upload-results'
+description: 'uploads our codeCov and jococo test results'
+inputs:
+  warnPR:
+    description: 'Update the failure logs on the PR for this job'
+    required: true
+    default: 'false'
+  repo-token:
+    description: 'The GITHUB_TOKEN secret'
+    required: false
+  test-type:
+    description: 'Type to lable this test as'
+    required: true
+  jdk-version:
+    description: 'jdk used for this test'
+    required: true
+  job-matrix-id:
+    description: 'The job-unique identifier for which test was run'
+    required: true
+  repo-path:
+    description: 'The job-unique identifier to use for uploading the results of this run into a google bucket'
+    required: true
+  identifier:
+    description: 'Identifier to use for finding the unique name for jobs in order to determine html logs location'
+    required: true
+  bot-comment-key:
+    description: 'Key to be used for commenting failed jobs on github PRs'
+    required: false
+
+runs:
+  using: "composite"
+  steps:
+    - name: Upload to codecov
+      run: bash <(curl -s https://raw.githubusercontent.com/broadinstitute/codecov-bash-uploader/main/codecov-verified.bash)
+      shell: bash
+    - name: Upload test results
+      if: always()
+      uses: actions/upload-artifact@v2
+      with:
+        name: test-results-${{ matrix.Java }}-${{ matrix.testType }}
+        path: build/reports/tests
+
+    - name: Upload Reports
+      id: uploadreports
+      run: |
+        gsutil -m cp -z html -z js -z xml -z css -r build/reports/tests gs:/${{ env.HELLBENDER_TEST_LOGS }}${{ inputs.repo-path }}/;
+        VIEW_URL=https://storage.googleapis.com${{ 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
+      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"
+        echo "${{ inputs.identifier }}"
+        #curl --get -Ss -H "Authorization: token ${GITHUB_TOKEN}" -H "Accept: application/vnd.github.v3+json" "${GITHUB_BASEURL}${GITHUB_API}?per_page=${INPUT_PER_PAGE:-H30}"
+        eval "$(curl --get -Ss -H "Authorization: token ${GITHUB_TOKEN}" -H "Accept: application/vnd.github.v3+json" "${GITHUB_BASEURL}${GITHUB_API}?per_page=${INPUT_PER_PAGE:-H30}" \
+        | 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' }}
+      env:
+        GITHUB_TOKEN: ${{ inputs.bot-comment-key }}
+        TEST_TYPE: ${{ inputs.test-type }}
+        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: ${{ inputs.jdk-version }}
+        ACTIONS_JOB_WEB_URL: https://github.com/${{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..45d126406d1
--- /dev/null
+++ b/.github/workflows/gatk-tests.yml
@@ -0,0 +1,313 @@
+name: Build and Test GATK 4
+on:
+  push:
+    branches: [ lb_github_actions ]
+  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:
+  buildDocker:
+    name: build docker images
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout gatk
+        uses: actions/checkout@v2
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - 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: Build and push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+#Run our non-docker tests
+  test:
+    runs-on: ubuntu-latest
+    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: 'Grant execute permission for gradlew'
+        run: chmod +x gradlew
+
+      - name: 'Compile with Gradle'
+        run: |
+          ./gradlew compileJava ; ./gradlew installDist
+
+      #Google Cloud stuff
+      - id: 'auth'
+        uses: google-github-actions/auth@v0
+        with:
+          credentials_json: ${{ secrets.GCP_CREDENTIALS }}
+          project_id: ${{ env.HELLBENDER_TEST_PROJECT }}
+          create_credentials_file: true
+
+      - name: "export the credentials for GATK tests"
+        run: echo "HELLBENDER_JSON_SERVICE_ACCOUNT_KEY=${{ steps.auth.outputs.credentials_file_path }}" >> $GITHUB_ENV
+
+      - name: 'Set up Cloud SDK'
+        uses: google-github-actions/setup-gcloud@v0
+
+      - name: pull lfs files
+        run: git lfs pull
+
+      - name: compile test code
+        run: ./gradlew compileTestJava
+
+      - name: run-tests
+        id: jacoco-tests
+        run: |
+          ./gradlew -Dscala.version=${{ 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.jacoco-tests.outcome != 'success' }}
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          jdk-version: ${{ matrix.Java }}
+          test-type: ${{ matrix.testType }}
+          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 }} build and test ${{ matrix.testType }}
+
+  testOnDocker:
+    needs: buildDocker
+    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: 'auth'
+        uses: google-github-actions/auth@v0
+        with:
+          credentials_json: ${{ secrets.GCP_CREDENTIALS }}
+          project_id: ${{ env.HELLBENDER_TEST_PROJECT }}
+          create_credentials_file: true
+
+      - name: "export the credentials for GATK tests"
+        run: echo "HELLBENDER_JSON_SERVICE_ACCOUNT_KEY=${{ steps.auth.outputs.credentials_file_path }}" >> $GITHUB_ENV
+
+      - name: 'Set up Cloud SDK'
+        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: pull docker
+        run: docker pull ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ github.sha }}
+
+      - 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: /broadinstitute/gatk/.github/actions/upload-results@lb_github_actions
+        if: always()
+        with:
+          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 }}
+          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}}
+
+
+  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: /broadinstitute/gatk/.github/actions/install-cromwell@lb_github_actions
+        with:
+          CROMWELL_VERSION: ${{ env.CROMWELL_VERSION }}
+
+      - name: Grant execute permission for gradlew
+        run: chmod +x gradlew
+
+      - name: Run WDL Generation Test
+        run: ./gradlew gatkWDLGenValidation
+
+  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: /broadinstitute/gatk/.github/actions/install-cromwell@lb_github_actions
+        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: "Installing GATK for tests"
+        run: |
+          ./gradlew assemble;
+          ./gradlew installDist;
+          echo "building a shadow jar for the wdl";
+          ./gradlew shadowJar;
+
+      - 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: ${{ matrix.wdlTest == 'RUN_CNN_WDL' }}
+        run: |
+          echo "Running CNN WDL";
+          bash scripts/cnn_variant_cromwell_tests/run_cnn_variant_wdl.sh;
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index b9e4195b256..00000000000
--- a/.travis.yml
+++ /dev/null
@@ -1,228 +0,0 @@
-language: java
-dist: bionic
-group: travis_lts
-git:
-  # We intentionally check out the entire repo history because we hit errors during the build if the most recent tag isn't in our history for `git describe`
-  depth: 9999999
-  lfs_skip_smudge: true
-jdk:
-  - openjdk8
-env:
-  matrix:
-  - SCALA_VERSION=2.11 TEST_TYPE=cloud UPLOAD=true TESTS_REQUIRE_GCLOUD=true
-  - SCALA_VERSION=2.11 TEST_TYPE=integration TEST_DOCKER=true TEST_VERBOSITY=minimal
-  - SCALA_VERSION=2.11 TEST_TYPE=unit TEST_DOCKER=true TEST_VERBOSITY=minimal
-  - SCALA_VERSION=2.11 TEST_TYPE=variantcalling TEST_DOCKER=true TEST_VERBOSITY=minimal
-  - SCALA_VERSION=2.11 TEST_TYPE=conda TEST_DOCKER=true TEST_VERBOSITY=minimal
-  - SCALA_VERSION=2.11 RUN_CNV_GERMLINE_COHORT_WDL=true TESTS_REQUIRE_GCLOUD=true
-  - SCALA_VERSION=2.11 RUN_CNV_GERMLINE_CASE_WDL=true TESTS_REQUIRE_GCLOUD=true
-  - SCALA_VERSION=2.11 RUN_CNV_SOMATIC_WDL=true TESTS_REQUIRE_GCLOUD=true
-  - SCALA_VERSION=2.11 RUN_M2_WDL=true TESTS_REQUIRE_GCLOUD=true
-  - SCALA_VERSION=2.11 RUN_CNN_WDL=true TESTS_REQUIRE_GCLOUD=true
-  - SCALA_VERSION=2.11 TEST_TYPE=wdlGen
-  global:
-  #gradle needs this
-  - TERM=dumb
-  #limit gradle jvm memory and disable daemon
-  - GRADLE_OPTS="-Xmx2048m -Dorg.gradle.daemon=false"
-  #google cloud stuff
-  - export CLOUDSDK_CONFIG=${PWD}/config
-  - export CLOUDSDK_CORE_DISABLE_PROMPTS=1
-  - export GCLOUD_HOME=$HOME/gcloud/google-cloud-sdk/bin
-  - export CLOUDSDK_PYTHON_SITEPACKAGES=1
-  - export GOOGLE_APPLICATION_CREDENTIALS=$TRAVIS_BUILD_DIR/servicekey.json
-  #hellbender specific variables
-  - 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
-  - HELLBENDER_JSON_SERVICE_ACCOUNT_KEY=servicekey.json
-  #Work around for https://github.com/googleapis/google-cloud-java/issues/5884
-  - export GOOGLE_CLOUD_PROJECT=$HELLBENDER_TEST_PROJECT
-  # For cromwell jar download
-  - export CROMWELL_JAR=$HOME/cromwell-51.jar
-  - export WOMTOOL_JAR=$HOME/womtool-51.jar
-matrix:
-  fast_finish: true
-  include:
-     - jdk: openjdk11
-       language: java
-       env: SCALA_VERSION=2.12 TEST_TYPE=integration TEST_VERBOSITY=minimal
-     - jdk: openjdk11
-       language: java
-       env: SCALA_VERSION=2.12 TEST_TYPE=unit TEST_VERBOSITY=minimal
-     - jdk: openjdk11
-       language: java
-       env: SCALA_VERSION=2.12 TEST_TYPE=cloud TESTS_REQUIRE_GCLOUD=true TEST_VERBOSITY=minimal
-before_cache:
-  - rm -f  $HOME/.gradle/caches/modules-2/modules-2.lock
-  - rm -fr $HOME/.gradle/caches/*/plugin-resolution/
-cache:
-  directories:
-    - $HOME/.gradle/caches/
-    - $HOME/.gradle/wrapper/
-    - $HOME/.m2
-    - $HOME/gcloud/
-    - $HOME/site-library
-before_install:
-  #skip push builds if there's an associated PR because we don't look at them anway
-- if [[ ${TRAVIS_EVENT_TYPE} == push ]];
-  then
-    PULL_REQUESTS=$( scripts/travis/check_for_pull_request );
-    if [[ $( grep -c "commits" <<< ${PULL_REQUESTS} ) -gt 0 ]];
-    then
-      travis_terminate 0;
-    fi;
-  fi;
-- if [[ $TRAVIS_SECURE_ENV_VARS == true ]]; then
-    echo "Logging in to dockerhub";
-    docker login --username=$DOCKER_SERVICE_LOGIN --password=$DOCKER_SERVICE_TOKEN;
-  fi
-- REPORT_PATH=${TRAVIS_BRANCH}_${TRAVIS_JOB_NUMBER};
-- if [[ $TRAVIS_SECURE_ENV_VARS == true && $TRAVIS_EVENT_TYPE != cron ]]; then
-    echo "Test report will be written to  https://storage.googleapis.com$HELLBENDER_TEST_LOGS$REPORT_PATH/tests/test/index.html";
-  fi;
-- if [[ ${TRAVIS_SECURE_ENV_VARS} == true ]]; then
-    if [[ ${TESTS_REQUIRE_GCLOUD} == true ]]; then
-      scripts/travis/install_and_authenticate_to_gcloud.sh;
-    fi;
-    openssl aes-256-cbc -K $encrypted_8ebb1ef83f64_key -iv $encrypted_8ebb1ef83f64_iv -in resources_for_CI/github_deploy_key.enc -out ~/.ssh/id_rsa -d;
-    chmod 600 ~/.ssh/id_rsa;
-    echo "Testing github authentication:";
-    ssh -T git@github.com;
-    echo "Done testing github authentication";
-  fi;
-# Download Cromwell jar -- if you change the version, please change the CROMWELL_JAR env variable above, too.
-- if [[ $TEST_TYPE == wdlGen || $RUN_CNV_GERMLINE_COHORT_WDL == true || $RUN_CNV_GERMLINE_CASE_WDL == true || $RUN_CNV_SOMATIC_WDL == true || $RUN_M2_WDL == true || $RUN_CNN_WDL == true ]]; then
-    wget -O $CROMWELL_JAR https://github.com/broadinstitute/cromwell/releases/download/51/cromwell-51.jar;
-    wget -O $WOMTOOL_JAR https://github.com/broadinstitute/cromwell/releases/download/51/womtool-51.jar;
-  fi;
-# Download git lfs files
-- git lfs
-- git lfs install
-- git lfs fetch
-- git lfs checkout
-# Disable services enabled by default to free a bit of memory
-# http://docs.travis-ci.com/user/database-setup/#MySQL
-- sudo /etc/init.d/mysql stop
-- sudo /etc/init.d/postgresql stop
-install:
-- if [[ $TRAVIS_SECURE_ENV_VARS == false && $TEST_TYPE == cloud ]]; then
-    echo "Can't run cloud tests without keys so don't bother building";
-  elif [[ $TEST_DOCKER == true ]]; then
-    echo "Skip the install because we're doing a docker build";
-  else
-    ./gradlew assemble;
-    ./gradlew installDist;
-    if [[ $RUN_CNV_GERMLINE_COHORT_WDL == true || $RUN_CNV_GERMLINE_CASE_WDL == true || $RUN_CNV_SOMATIC_WDL == true || $RUN_M2_WDL == true || $RUN_CNN_WDL == true ]]; then
-      echo "building a shadow jar for the wdl";
-      ./gradlew shadowJar;
-    elif [[ $TEST_TYPE == cloud ]]; then
-      echo "building a spark jar for the dataproc tests";
-      ./gradlew sparkjar;
-    fi;
-  fi;
-script:
-# run a basic sanity check to be sure that gatk doesn't explode
-# run tests
-# Because the docker build for GATK doesn't include the test code or the src files we have to manually collect them into a location to be mounted in for performing tests
-- if [[ $TRAVIS_EVENT_TYPE == cron ]]; then
-    echo "Not running any tests for nightly builds";
-  elif [[ $TEST_TYPE == wdlGen ]]; then
-    ./gradlew gatkWDLGenValidation;
-  elif [[ $TRAVIS_SECURE_ENV_VARS == false && $TEST_TYPE == cloud ]]; then
-    echo "Can't run cloud tests without keys so don't run tests";
-  elif [[ $RUN_CNV_GERMLINE_COHORT_WDL == true ]]; then
-    echo "Running CNV germline cohort workflow";
-    travis_wait 60 bash scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh COHORT;
-  elif [[ $RUN_CNV_GERMLINE_CASE_WDL == true ]]; then
-    echo "Running CNV germline case workflow";
-    travis_wait 60 bash scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh CASE;
-  elif [[ $RUN_CNV_SOMATIC_WDL == true ]]; then
-    echo "Running CNV somatic workflows";
-    travis_wait 60 bash scripts/cnv_cromwell_tests/somatic/run_cnv_somatic_workflows.sh;
-  elif [[ $RUN_M2_WDL == true ]]; then
-    echo "Deleting some unused files before running M2 WDL...";
-    rm -Rf src/test/resources/large/VQSR;
-    echo "Running M2 WDL";
-    travis_wait 60 sudo bash scripts/m2_cromwell_tests/run_m2_wdl.sh;
-  elif [[ $RUN_CNN_WDL == true ]]; then
-    echo "Running CNN WDL";
-    travis_wait 60 sudo bash scripts/cnn_variant_cromwell_tests/run_cnn_variant_wdl.sh;
-  elif [[ $TEST_DOCKER == true ]]; then
-    echo "Building docker image and running appropriate tests..." ;
-    if [ ${TRAVIS_PULL_REQUEST} != false ]; then
-      sudo bash build_docker.sh  -e FETCH_HEAD -s -u -t ${TRAVIS_PULL_REQUEST};
-      DOCKER_TAG=FETCH_HEAD;
-    else
-      echo ${TRAVIS_COMMIT};
-      sudo bash build_docker.sh  -e ${TRAVIS_COMMIT} -s -u;
-      DOCKER_TAG=$TRAVIS_COMMIT;
-    fi;
-    sudo docker images;
-    echo ${TEST_TYPE};
-    sudo ./gradlew clean shadowTestClassJar shadowTestJar;
-    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 .;
-    sudo docker run -v $(pwd):/gatkCloneMountPoint:cached -v $(pwd)/testJars:/jars:cached --rm -e "scala.version=${SCALA_VERSION}" -e "TEST_VERBOSITY=minimal" -e "TEST_TYPE=${TEST_TYPE}" -t broadinstitute/gatk:${DOCKER_TAG} bash --init-file /gatk/gatkenv.rc /root/run_unit_tests.sh;
-    TEST_EXIT_VALUE=$?;
-    sudo mkdir build/reports/tests/test && sudo cp -rp build/reports/tests/testOnPackagedReleaseJar/* build/reports/tests/test && sudo rm -r build/reports/tests/testOnPackagedReleaseJar;
-    $( exit ${TEST_EXIT_VALUE} );
-  else
-    ./gatk PrintReads -I src/test/resources/NA12878.chr17_69k_70k.dictFix.bam -O output.bam;
-    export GATK_LAUNCH_SCRIPT="$(pwd)/gatk";
-    travis_wait 50 ./gradlew -Dscala.version=${SCALA_VERSION} jacocoTestReport;
-  fi;
-# This creates and uploads the gatk zip file to the nightly build bucket, only keeping the 10 newest entries
-# This also constructs the Docker image and uploads it to https://cloud.docker.com/u/broadinstitute/repository/docker/broadinstitute/gatk-nightly/
-- if [[ $TRAVIS_BRANCH == master && $TRAVIS_EVENT_TYPE == cron && $UPLOAD == true ]]; then
-  $GCLOUD_HOME/gcloud components -q update gsutil;
-  gsutil ls -l gs://gatk-nightly-builds | grep gatk | sort -r -k 2 | grep -o '\S\+$' | tail -n +11 | xargs -I {} gsutil rm {};
-  ./gradlew bundle;
-  ZIP_FILE="$(ls build/ | grep '^gatk.*.zip$' | grep -iv python)";
-  echo "Uploading zip to gs://gatk-nightly-builds/";
-  $GCLOUD_HOME/gsutil -m cp build/$ZIP_FILE gs://gatk-nightly-builds/"$(date +%Y-%m-%d)"-$ZIP_FILE;
-
-  bash build_docker.sh  -e ${TRAVIS_COMMIT} -s -u;
-  DOCKER_TAG=$(docker images -q | head -n 1);
-  DATE=$(date +%Y-%m-%d);
-  DOCKER_NIGHTLY_TAG=broadinstitute/gatk-nightly:$DATE-$(git describe)-NIGHTLY-SNAPSHOT;
-  DOCKER_NIGHTLY_TAG_LATEST=broadinstitute/gatk-nightly:latest;
-
-  echo "Pushing Nightly Docker image";
-  docker tag $DOCKER_TAG $DOCKER_NIGHTLY_TAG;
-  docker tag $DOCKER_TAG $DOCKER_NIGHTLY_TAG_LATEST;
-  docker push $DOCKER_NIGHTLY_TAG;
-  docker push $DOCKER_NIGHTLY_TAG_LATEST;
-  fi;
-
-after_success:
-# - bash <(curl -s https://codecov.io/bash)
-- if [[ $TRAVIS_BRANCH == master && $UPLOAD == true ]]; then ./gradlew uploadArchives; fi;
-# if this is actually a commit to master and not a pull request build into master, then publish master-snapshot
-- if [[ $TRAVIS_BRANCH == master && $TRAVIS_PULL_REQUEST == false && $UPLOAD == true ]]; then
-    git tag master;
-    ./gradlew uploadArchives; 
-  fi;
-after_failure:
-- test -f hs_err_*.log && cat hs_err_*.log
-- dmesg | tail -100
-- export FAILED=true
-after_script:
-- if [[ $TRAVIS_SECURE_ENV_VARS == true && $TRAVIS_EVENT_TYPE != cron ]]; then
-    if [[ ${TESTS_REQUIRE_GCLOUD} != "true" ]]; then
-      scripts/travis/install_and_authenticate_to_gcloud.sh;
-    fi;
-    $GCLOUD_HOME/gsutil -m cp -z html -z js -z xml -z css -r build/reports/tests gs:/$HELLBENDER_TEST_LOGS$REPORT_PATH/;
-    echo "See the test report at https://storage.googleapis.com$HELLBENDER_TEST_LOGS$REPORT_PATH/tests/test/index.html";
-    if [[ ${FAILED} == true && ${TRAVIS_PULL_REQUEST} != false && -d build/reports/tests ]]; then
-      pip install --user PyGithub;
-      python scripts/travis/Reporter.py https://storage.googleapis.com$HELLBENDER_TEST_LOGS$REPORT_PATH/tests/test/index.html;
-    fi
-  fi;
-
diff --git a/scripts/cnn_variant_cromwell_tests/run_cnn_variant_wdl.sh b/scripts/cnn_variant_cromwell_tests/run_cnn_variant_wdl.sh
index fd7ba3355e6..18a4d824c3d 100644
--- a/scripts/cnn_variant_cromwell_tests/run_cnn_variant_wdl.sh
+++ b/scripts/cnn_variant_cromwell_tests/run_cnn_variant_wdl.sh
@@ -4,7 +4,7 @@ set -e
 script_path=$( 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..c6fb86704ac 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/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",
+  "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..b2ae5ca0a96 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/build/broadinstitute/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 2507e3e876d..8dc9deb5884 100644
--- a/scripts/m2_cromwell_tests/test_mitochondria_m2_wdl.json
+++ b/scripts/m2_cromwell_tests/test_mitochondria_m2_wdl.json
@@ -1,26 +1,26 @@
 {
   "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.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.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.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
diff --git a/src/test/java/org/broadinstitute/hellbender/engine/FeatureInputUnitTest.java b/src/test/java/org/broadinstitute/hellbender/engine/FeatureInputUnitTest.java
index a3aec293eec..78627513d1e 100644
--- a/src/test/java/org/broadinstitute/hellbender/engine/FeatureInputUnitTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/engine/FeatureInputUnitTest.java
@@ -143,6 +143,7 @@ public void testGcsPathAndName( final String argWithTags, final String inputValu
 
         Assert.assertEquals(gcsInput.getFeaturePath(), expectedFeaturePath, "wrong featurePath");
         Assert.assertEquals(gcsInput.getName(), expectedLogicalName, "wrong logical name");
+        Assert.fail();
     }
 
     @Test(dataProvider = "HdfsPathAndNameData")