fix(preprocessor): matching pattern for GVCFBlock in the header #128
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name: Preprocessor CI | |
on: | |
workflow_dispatch: | |
branches: | |
- '*' | |
push: | |
branches: | |
- '*' | |
paths: | |
- '.github/workflows/ci-preprocessor.yml' | |
- 'preprocessor/**' | |
# cancel current build on push from the same PR, branch or tag (https://stackoverflow.com/a/72408109/1063501) | |
concurrency: | |
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
cancel-in-progress: true | |
env: | |
BCFTOOLS_VERSION: '1.20' | |
HTSLIB_VERSION: '1.20' | |
REFERENCE_FASTA_ZENODO_ID: 7288118 | |
TOOLS_DIR: /home/runner/work/PharmCAT/PharmCAT/tools | |
jobs: | |
build: | |
name: Build project | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout code | |
uses: actions/checkout@v4 | |
- name: Cache bcftools | |
id: cache-bcftools | |
uses: actions/cache@v4 | |
with: | |
path: ${{ env.TOOLS_DIR }}/bcftools | |
key: bcftools-${{ env.BCFTOOLS_VERSION }} | |
- name: Install bcftools | |
if: steps.cache-bcftools.outputs.cache-hit != 'true' | |
run: | | |
wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2 | |
tar -xjf bcftools-${BCFTOOLS_VERSION}.tar.bz2 | |
cd bcftools-${BCFTOOLS_VERSION} | |
./configure --prefix ${TOOLS_DIR}/bcftools | |
make | |
make install | |
- name: Cache htslib | |
id: cache-htslib | |
uses: actions/cache@v4 | |
with: | |
path: ${{ env.TOOLS_DIR }}/htslib | |
key: htslib-${{ env.HTSLIB_VERSION }} | |
- name: Install htslib | |
if: steps.cache-htslib.outputs.cache-hit != 'true' | |
run: | | |
wget https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2 | |
tar -xjf htslib-${HTSLIB_VERSION}.tar.bz2 | |
cd htslib-${HTSLIB_VERSION} | |
./configure --prefix ${TOOLS_DIR}/htslib | |
make | |
make install | |
- name: Add tools to path | |
run: echo "${TOOLS_DIR}/bcftools/bin:${TOOLS_DIR}/htslib/bin" >> $GITHUB_PATH | |
# need JDK present for tests | |
- name: Set up JDK | |
uses: actions/setup-java@v4 | |
with: | |
distribution: 'temurin' | |
java-version: '17' | |
- name: Set up python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: '3.10' | |
cache: 'pip' | |
- name: Install python dependencies | |
run: pip3 install -r preprocessor/requirements.txt | |
- name: Install pytest | |
run: pip3 install pytest pytest-cov pytest-github-actions-annotate-failures | |
- name: Cache reference FASTA | |
id: cache-ref-fasta | |
uses: actions/cache@v4 | |
with: | |
path: | | |
reference.fna.bgz | |
reference.fna.bgz.fai | |
reference.fna.bgz.gzi | |
key: ref-fasta-${{ env.REFERENCE_FASTA_ZENODO_ID }} | |
- name: Download reference FASTA | |
if: steps.cache-ref-fasta.outputs.cache-hit != 'true' | |
run: | | |
wget https://zenodo.org/record/${REFERENCE_FASTA_ZENODO_ID}/files/GRCh38_reference_fasta.tar | |
tar -xf GRCh38_reference_fasta.tar | |
rm -f GRCh38_reference_fasta.tar | |
# wait a bit on a release commit to give release action time to upload the resources necessary for test | |
- name: Sleep for 60 seconds | |
run: sleep 60s | |
shell: bash | |
if: ${{ startsWith(github.event.head_commit.message, 'chore(release)') }} | |
- name: Run preprocessor tests | |
run: python3 -m pytest --cov-config=../.coveragerc --cov-report=xml --cov=preprocessor | |
working-directory: preprocessor | |
- name: Codecov | |
uses: codecov/codecov-action@v3 | |
with: | |
files: preprocessor/coverage-python.xml | |
flags: Preprocessor | |
- name: Send Slack notification on failure | |
if: failure() | |
uses: slackapi/slack-github-action@v1 | |
with: | |
channel-id: 'dev' | |
payload: | | |
{ | |
"attachments": [{ | |
"color": "#ff0000", | |
"blocks": [ | |
{ | |
"type": "section", | |
"text": { | |
"type": "mrkdwn", | |
"text": ":stop: <https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}|FAILED ${{ github.workflow }}!>" | |
} | |
}, | |
{ | |
"type": "section", | |
"text": { | |
"type": "mrkdwn", | |
"text": "Triggered by ${{ github.event_name }} on <${{ github.event.pull_request.html_url || github.event.head_commit.url }}|${{ github.ref_name }}> by ${{ github.actor }}." | |
} | |
}, | |
{ | |
"type": "context", | |
"elements": [ | |
{ | |
"type": "mrkdwn", | |
"text": "Last commit:\n${{ github.event.head_commit.message }}" | |
} | |
] | |
} | |
] | |
}] | |
} | |
env: | |
SLACK_BOT_TOKEN: ${{ secrets.SLACK_NOTIFICATIONS_BOT_TOKEN }} |