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MarkDuplicates flow options now start with FLOW_ #217

MarkDuplicates flow options now start with FLOW_

MarkDuplicates flow options now start with FLOW_ #217

Workflow file for this run

name: Cloud Tests
on:
push:
branches:
- 'master'
pull_request:
workflow_dispatch:
env:
PICARD_TEST_INPUTS: gs://hellbender/test/resources/
PICARD_TEST_STAGING: gs://hellbender-test-logs/staging/
PICARD_TEST_LOGS: /hellbender-test-logs/build_reports/
PICARD_TEST_PROJECT: broad-dsde-dev
jobs:
## This workaround is necessary since there is no equivalent to the old TRAVIS_SECURE_ENVIRONMENT variable that indicated
## if a run was privileged and had secrets. Since the GCP credentials are necessary for all tests in order to upload their,
## results that makes them a reasonable proxy for testing the credentials of this entire execution. https://github.com/actions/runner/issues/520
check-secrets:
name: check if the environment has privileges
outputs:
google-credentials: ${{ steps.google-credentials.outputs.defined }}
runs-on: ubuntu-latest
steps:
- id: google-credentials
env:
GCP_CREDENTIALS: ${{ secrets.GCP_CREDENTIALS }}
if: "${{ env.GCP_CREDENTIALS != '' }}"
run: echo defined=true >> $GITHUB_OUTPUT
test:
runs-on: ubuntu-latest
needs: check-secrets
strategy:
matrix:
java: [ 17 ]
run_barclay_tests: [true, false]
experimental: [ false ]
fail-fast: false
continue-on-error: ${{ matrix.experimental }}
name: Java ${{ matrix.Java }}, Barclay=${{ matrix.run_barclay_tests}} cloud tests
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
- name: 'Set up java ${{ matrix.Java }}'
uses: actions/setup-java@v3
with:
java-version: ${{ matrix.Java }}
distribution: 'temurin'
cache: gradle
- name: 'Compile with Gradle'
run: |
./gradlew compileJava
./gradlew installDist
#Google Cloud stuff
- id: 'gcloud-auth'
if: needs.check-secrets.outputs.google-credentials == 'true'
uses: google-github-actions/auth@v0
with:
credentials_json: ${{ secrets.GCP_CREDENTIALS }}
project_id: ${{ env.PICARD_TEST_PROJECT }}
create_credentials_file: true
- name: 'Set up Cloud SDK'
if: needs.check-secrets.outputs.google-credentials == 'true'
uses: google-github-actions/setup-gcloud@v2
- name: compile test code
if: needs.check-secrets.outputs.google-credentials == 'true'
run: ./gradlew compileTestJava
- name: Run tests
if: needs.check-secrets.outputs.google-credentials == 'true'
env:
TEST_TYPE: cloud
run: |
if [[ ${{matrix.run_barclay_tests}} == true ]]; then
echo "Running tests using the Barclay command line parser."
./gradlew barclayTest
else
echo "Running tests using the legacy Picard command line parser."
./gradlew jacocoTestReport
fi
- name: Upload test results
if: always()
uses: actions/upload-artifact@v3
with:
name: cloud-test-results-${{ matrix.Java }}-barclay-${{ matrix.run_barclay_tests}}
path: build/reports/tests