Update syntax docs #7447
Workflow file for this run
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name: Nextflow CI | |
# read more here: https://help.github.com/en/articles/workflow-syntax-for-github-actions#on | |
# Note: We don't use the `on: path` option for docs, | |
# because the Build steps are *required* tests. | |
# Instead, we trigger + skip the tests if the only changes | |
# are in the docs folder. GitHub treats this as passing. | |
on: | |
push: | |
branches: | |
- 'master' | |
- 'test*' | |
- 'dev*' | |
- 'STABLE-*' | |
pull_request: | |
types: [opened, reopened, synchronize] | |
workflow_dispatch: | |
jobs: | |
build: | |
name: Build | |
runs-on: ubuntu-latest | |
timeout-minutes: 90 | |
strategy: | |
fail-fast: false | |
matrix: | |
java_version: [17, 23] | |
steps: | |
- name: Checkout | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: 1 | |
submodules: true | |
- name: Get the commit message | |
id: get_commit_message | |
run: | | |
if [ "${{ github.event_name }}" = "pull_request" ]; then | |
echo "GitHub event=pull_request" | |
COMMIT_SHA=${{ github.event.pull_request.head.sha }} | |
COMMIT_MESSAGE=$(curl -s \ | |
-H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \ | |
https://api.github.com/repos/${{ github.repository }}/commits/$COMMIT_SHA | jq -r '.commit.message') | |
echo "Commit message=$COMMIT_MESSAGE" | head -n 1 | |
echo "commit_message=$COMMIT_MESSAGE" | head -n 1 >> $GITHUB_OUTPUT | |
else | |
echo "GitHub event=${{ github.event_name }}" | |
echo "Commit message=${{ github.event.head_commit.message }}" | head -n 1 | |
echo "commit_message=${{ github.event.head_commit.message }}" | head -n 1 >> $GITHUB_OUTPUT | |
fi | |
- name: Get changed files | |
id: changed-files | |
uses: tj-actions/changed-files@v43 | |
with: | |
files_ignore: docs/** | |
- name: List all changed files | |
env: | |
ALL_CHANGED_FILES: ${{ steps.changed-files.outputs.all_changed_files }} | |
run: | | |
for file in ${ALL_CHANGED_FILES}; do | |
echo "$file was changed" | |
done | |
- name: Setup env | |
if: steps.changed-files.outputs.any_changed == 'true' | |
run: | | |
rm -f $HOME/.gitconfig; | |
mkdir -p "$HOME/.nextflow"; | |
echo "providers.github.auth='$NXF_GITHUB_ACCESS_TOKEN'" > "$HOME/.nextflow/scm" | |
env: | |
NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }} | |
- name: Setup Java ${{ matrix.java_version }} | |
if: steps.changed-files.outputs.any_changed == 'true' | |
uses: actions/setup-java@v4 | |
with: | |
java-version: ${{matrix.java_version}} | |
distribution: 'temurin' | |
architecture: x64 | |
cache: gradle | |
- name: Compile | |
if: steps.changed-files.outputs.any_changed == 'true' | |
run: make assemble | |
- name: Test | |
if: steps.changed-files.outputs.any_changed == 'true' | |
run: | | |
env | sort | |
# configure test env | |
if [[ "$GOOGLE_SECRET" ]]; then | |
echo $GOOGLE_SECRET | base64 -d > $PWD/google_credentials.json | |
export GOOGLE_APPLICATION_CREDENTIALS=$PWD/google_credentials.json | |
fi | |
# run tests | |
make test | |
env: | |
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
NXF_BITBUCKET_ACCESS_TOKEN: ${{ secrets.NXF_BITBUCKET_ACCESS_TOKEN }} | |
NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }} | |
NXF_GITLAB_ACCESS_TOKEN: ${{ secrets.NXF_GITLAB_ACCESS_TOKEN }} | |
NXF_AZURE_REPOS_TOKEN: ${{ secrets.NXF_AZURE_REPOS_TOKEN }} | |
GOOGLE_SECRET: ${{ secrets.GOOGLE_SECRET }} | |
AZURE_STORAGE_ACCOUNT_NAME: nfazurestore | |
AZURE_STORAGE_ACCOUNT_KEY: ${{ secrets.AZURE_STORAGE_ACCOUNT_KEY }} | |
AZURE_BATCH_ACCOUNT_NAME: nfbatchtest | |
AZURE_BATCH_ACCOUNT_KEY: ${{ secrets.AZURE_BATCH_ACCOUNT_KEY }} | |
- name: Publish tests report | |
uses: actions/upload-artifact@v4 | |
if: steps.changed-files.outputs.any_changed == 'true' && always() | |
with: | |
name: report-unit-tests-jdk-${{ matrix.java_version }} | |
path: | | |
**/build/reports/tests/test | |
outputs: | |
any_changed: ${{ steps.changed-files.outputs.any_changed }} | |
commit_message: ${{ steps.get_commit_message.outputs.commit_message }} | |
test: | |
if: ${{ !contains(needs.build.outputs.commit_message, '[ci fast]') && needs.build.outputs.any_changed == 'true' }} | |
needs: build | |
runs-on: ubuntu-latest | |
timeout-minutes: 90 | |
strategy: | |
fail-fast: false | |
matrix: | |
java_version: [17, 23] | |
test_mode: ["test_integration", "test_docs", "test_aws", "test_azure", "test_google", "test_wave"] | |
steps: | |
- name: Checkout | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: 1 | |
submodules: true | |
- name: Setup env | |
run: | | |
rm -f $HOME/.gitconfig; | |
mkdir -p "$HOME/.nextflow"; | |
echo "providers.github.auth='$NXF_GITHUB_ACCESS_TOKEN'" > "$HOME/.nextflow/scm" | |
env: | |
NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }} | |
- name: Setup Java ${{ matrix.java_version }} | |
uses: actions/setup-java@v4 | |
with: | |
java-version: ${{matrix.java_version}} | |
distribution: 'temurin' | |
architecture: x64 | |
cache: gradle | |
- name: Run tests | |
run: | | |
env | sort | |
# configure test env | |
if [[ "$GOOGLE_SECRET" ]]; then | |
echo $GOOGLE_SECRET | base64 -d > $PWD/google_credentials.json | |
export GOOGLE_APPLICATION_CREDENTIALS=$PWD/google_credentials.json | |
fi | |
cat $HOME/.nextflow/scm | |
make clean assemble install | |
bash test-ci.sh | |
env: | |
TEST_JDK: ${{ matrix.java_version }} | |
TEST_MODE: ${{ matrix.test_mode }} | |
GRADLE_OPTS: '-Dorg.gradle.daemon=false' | |
TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }} | |
AWS_DEFAULT_REGION: eu-west-1 | |
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
NXF_BITBUCKET_ACCESS_TOKEN: ${{ secrets.NXF_BITBUCKET_ACCESS_TOKEN }} | |
NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }} | |
NXF_GITLAB_ACCESS_TOKEN: ${{ secrets.NXF_GITLAB_ACCESS_TOKEN }} | |
NXF_AZURE_REPOS_TOKEN: ${{ secrets.NXF_AZURE_REPOS_TOKEN }} | |
GOOGLE_SECRET: ${{ secrets.GOOGLE_SECRET }} | |
AZURE_STORAGE_ACCOUNT_NAME: nfazurestore | |
AZURE_STORAGE_ACCOUNT_KEY: ${{ secrets.AZURE_STORAGE_ACCOUNT_KEY }} | |
AZURE_BATCH_ACCOUNT_NAME: nfbatchtest | |
AZURE_BATCH_ACCOUNT_KEY: ${{ secrets.AZURE_BATCH_ACCOUNT_KEY }} | |
- name: Tar integration tests | |
if: always() | |
run: tar -cvf integration-tests.tar tests/checks | |
- name: Publish tests report | |
uses: actions/upload-artifact@v4 | |
if: always() | |
with: | |
name: report-${{ matrix.test_mode }}-jdk-${{ matrix.java_version }} | |
path: | | |
validation/**/* | |
validation/**/.* | |
integration-tests.tar | |
test-e2e: | |
if: ${{ contains(needs.build.outputs.commit_message,'[e2e stage]') || contains(needs.build.outputs.commit_message,'[e2e prod]') }} | |
needs: build | |
runs-on: ubuntu-latest | |
timeout-minutes: 10 | |
permissions: | |
actions: write # Allow writing to actions | |
contents: write # Allow writing to repository contents | |
steps: | |
- name: Checkout | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: 1 | |
submodules: true | |
- name: Setup Java 17 | |
uses: actions/setup-java@v4 | |
with: | |
java-version: 17 | |
distribution: 'temurin' | |
architecture: x64 | |
cache: gradle | |
- name: Setup env | |
run: | | |
wget -q -O wave https://github.com/seqeralabs/wave-cli/releases/download/v1.4.1/wave-1.4.1-linux-x86_64 | |
chmod +x wave | |
mv wave /usr/local/bin/ | |
echo "COMMIT_MESSAGE=\"${{ needs.build.outputs.commit_message }}\"" >> $GITHUB_ENV | |
- name : Docker Login to Seqera public CR | |
uses : docker/login-action@v3 | |
with : | |
registry : "public.cr.seqera.io" | |
username : "public-cr-admin" | |
password : ${{ secrets.SEQERA_PUBLIC_CR_PASSWORD }} | |
- name: Launch tests | |
run: | | |
cd test-e2e | |
bash run.sh | |
env: | |
GITHUB_TOKEN: ${{ secrets.AUTOMATION_GITHUB_TOKEN }} | |
GRADLE_OPTS: '-Dorg.gradle.daemon=false' |