Test and configure unit test #38
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| # See the NOTICE file distributed with this work for additional information | |
| # regarding copyright ownership. | |
| # | |
| # Licensed under the Apache License, Version 2.0 (the "License"); | |
| # you may not use this file except in compliance with the License. | |
| # You may obtain a copy of the License at | |
| # http://www.apache.org/licenses/LICENSE-2.0 | |
| # | |
| # Unless required by applicable law or agreed to in writing, software | |
| # distributed under the License is distributed on an "AS IS" BASIS, | |
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | |
| # See the License for the specific language governing permissions and | |
| # limitations under the License. | |
| name: unit-test | |
| on: [pull_request] | |
| env: | |
| ENSEMBL_ROOT_DIR: repos | |
| jobs: | |
| ensembl_variation_utils: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash | |
| services: | |
| mysql: | |
| image: mysql:8.0 | |
| env: | |
| MYSQL_ROOT_PASSWORD: '' | |
| MYSQL_ALLOW_EMPTY_PASSWORD: true | |
| ports: | |
| - 3306:3306 | |
| options: >- | |
| --health-cmd="mysqladmin ping" | |
| --health-interval=10s | |
| --health-timeout=5s | |
| --health-retries=3 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: wait for MySQL | |
| run: | | |
| while ! mysqladmin ping -h"127.0.0.1" -P3306 --silent; do | |
| sleep 1 | |
| done | |
| - name: load databases | |
| run: | | |
| mysql -h 127.0.0.1 -u root -e 'CREATE DATABASE ensembl_genome_metadata;' | |
| mysql -h 127.0.0.1 -u root ensembl_genome_metadata < src/python/tests/variation_utils/data/ensembl_genome_metadata.dump | |
| mysql -h 127.0.0.1 -u root -e 'CREATE DATABASE homo_sapiens_core_110_38;' | |
| mysql -h 127.0.0.1 -u root homo_sapiens_core_110_38 < src/python/tests/variation_utils/data/homo_sapiens_core_110_38.dump | |
| - name: pytest | |
| run: | | |
| pip install coverage | |
| coverage run -m pytest | |
| coverage lcov -o coverage.lcov | |
| - name: Add coverage reports | |
| if: ${{ github.event_name == 'pull_request' }} | |
| continue-on-error: true | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| bash .github/scripts/py_coverage_comment.sh coverage.lcov | |
| vcf_prepper: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash | |
| working-directory: nextflow/vcf_prepper | |
| services: | |
| mysql: | |
| image: mysql:8.0 | |
| env: | |
| MYSQL_ROOT_PASSWORD: '' | |
| MYSQL_ALLOW_EMPTY_PASSWORD: true | |
| ports: | |
| - 3306:3306 | |
| options: >- | |
| --health-cmd="mysqladmin ping" | |
| --health-interval=10s | |
| --health-timeout=5s | |
| --health-retries=3 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/checkout@v4 | |
| with: | |
| repository: Ensembl/ensembl-vep | |
| ref: main | |
| path: 'nextflow/vcf_prepper/repos/ensembl-vep' | |
| - uses: actions/checkout@v4 | |
| with: | |
| repository: Ensembl/ensembl | |
| ref: main | |
| path: 'nextflow/vcf_prepper/repos/ensembl' | |
| - uses: actions/checkout@v4 | |
| with: | |
| repository: Ensembl/ensembl-variation | |
| ref: main | |
| path: 'nextflow/vcf_prepper/repos/ensembl-variation' | |
| - uses: actions/checkout@v4 | |
| with: | |
| repository: Ensembl/VEP_plugins | |
| ref: main | |
| path: 'nextflow/vcf_prepper/repos/VEP_plugins' | |
| - uses: actions/setup-java@v2 | |
| with: | |
| java-version: '17' | |
| distribution: 'adopt' | |
| - uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: '24.04.3' | |
| - name: wait for MySQL | |
| run: | | |
| while ! mysqladmin ping -h"127.0.0.1" -P3306 --silent; do | |
| sleep 1 | |
| done | |
| - name: load databases | |
| run: | | |
| mysql -h 127.0.0.1 -u root -e 'CREATE DATABASE ensembl_genome_metadata;' | |
| mysql -h 127.0.0.1 -u root ensembl_genome_metadata < tests/testdata/ensembl_genome_metadata.dump | |
| mysql -h 127.0.0.1 -u root -e 'CREATE DATABASE homo_sapiens_core_110_38;' | |
| mysql -h 127.0.0.1 -u root homo_sapiens_core_110_38 < tests/testdata/homo_sapiens_core_110_38.dump | |
| - name: setup tools | |
| run: | | |
| # install pre-requisites | |
| sudo apt-get update | |
| sudo apt-get install -y \ | |
| build-essential \ | |
| zlib1g-dev \ | |
| libbz2-dev \ | |
| liblzma-dev \ | |
| libcurl4-openssl-dev \ | |
| libssl-dev | |
| # install htslib | |
| HTSLIB_VERSION=1.19 | |
| wget -q https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2 | |
| tar -xjf htslib-${HTSLIB_VERSION}.tar.bz2 | |
| cd htslib-${HTSLIB_VERSION} | |
| ./configure --prefix=/usr/local | |
| make -j$(nproc) | |
| sudo make install | |
| # install bcftools | |
| BCFTOOLS_VERSION=1.19 | |
| 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=/usr/local | |
| make -j$(nproc) | |
| sudo make install | |
| # install ucsc tools | |
| wget https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed | |
| chmod +x bedToBigBed | |
| mv bedToBigBed /usr/local/bin | |
| wget https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig | |
| chmod +x wigToBigWig | |
| mv wigToBigWig /usr/local/bin | |
| # add to path | |
| echo "PATH=/usr/local/bin:$PATH" >> $GITHUB_ENV | |
| - name: setup nf-test | |
| run: | | |
| wget -qO- https://get.nf-test.com | bash | |
| sudo mv nf-test /usr/local/bin/ | |
| - name: setup Python dependencies | |
| run: | | |
| python3 -m pip install ${GITHUB_WORKSPACE}/src/python | |
| python3 -m pip install -r requirements.txt | |
| - name: setup Perl dependencies | |
| run: | | |
| BIOPERL_VERSION=release-1-6-924 | |
| HTSLIB_VERSION=1.19 | |
| BIOHTS_VERSION=2.11 | |
| LIB_DIR=${GITHUB_WORKSPACE}/nextflow/vcf_prepper/repos/ensembl-vep/modules/ | |
| # add module path to PERL5LIB | |
| for lib_path in ${GITHUB_WORKSPACE}/nextflow/vcf_prepper/repos/ensembl*/modules | |
| do | |
| PERL5LIB=${lib_path}:$PERL5LIB | |
| done | |
| export PERL5LIB | |
| # install Module::Build - needed for Bio::DB::HTS | |
| sudo apt-get update | |
| sudo apt-get install -y cpanminus | |
| cpanm Module::Build | |
| # install Bioperl - needed for Bio::DB::HTS | |
| wget https://github.com/bioperl/bioperl-live/archive/$BIOPERL_VERSION.zip | |
| unzip $BIOPERL_VERSION.zip | |
| rsync -r bioperl-live-$BIOPERL_VERSION/Bio ${LIB_DIR}/ | |
| # install Bio::DB::HTS | |
| wget https://github.com/Ensembl/Bio-DB-HTS/archive/$BIOHTS_VERSION.zip | |
| unzip $BIOHTS_VERSION.zip | |
| cd Bio-DB-HTS-$BIOHTS_VERSION | |
| perl Build.PL --htslib ${GITHUB_WORKSPACE}/nextflow/vcf_prepper/htslib-${HTSLIB_VERSION} | |
| ./Build | |
| rsync -r lib/Bio ${LIB_DIR}/ | |
| rsync blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so ${LIB_DIR}/ | |
| # add PERL5LIB to env variable | |
| echo "PERL5LIB=$PERL5LIB" >> $GITHUB_ENV | |
| - name: setup Rust dependencies | |
| run: | | |
| cargo build --manifest-path ${GITHUB_WORKSPACE}/src/rust/ensembl/vcf_to_bed/Cargo.toml | |
| cp ${GITHUB_WORKSPACE}/src/rust/ensembl/vcf_to_bed/target/debug/vcf_to_bed \ | |
| ${GITHUB_WORKSPACE}/nextflow/vcf_prepper/bin/vcf_to_bed | |
| cargo build --manifest-path ${GITHUB_WORKSPACE}/src/rust/ensembl/bed_to_wig/Cargo.toml | |
| cp ${GITHUB_WORKSPACE}/src/rust/ensembl/bed_to_wig/target/debug/bed_to_wig \ | |
| ${GITHUB_WORKSPACE}/nextflow/vcf_prepper/bin/bed_to_wig | |
| - name: test | |
| run: | | |
| export ENSEMBL_ROOT_DIR=${GITHUB_WORKSPACE}/nextflow/vcf_prepper/repos | |
| export FTP_NFS_DIR=${GITHUB_WORKSPACE}/nextflow/vcf_prepper/tests/testdata | |
| export OLD_FTP_NFS_DIR=${GITHUB_WORKSPACE}/nextflow/vcf_prepper/tests/testdata | |
| export PLUGIN_DATA_DIR=${GITHUB_WORKSPACE}/nextflow/vcf_prepper/modules/local/vep_config/plugins/tests/testdata | |
| sed -i -e 's|\${BASE_DIR}|'"$GITHUB_WORKSPACE"'|g' ${GITHUB_WORKSPACE}/nextflow/vcf_prepper/tests/testdata/input_config.json | |
| sed -i -e 's|\${BASE_DIR}|'"$GITHUB_WORKSPACE"'|g' ${GITHUB_WORKSPACE}/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/test_vep_config.ini | |
| nf-test test . \ | |
| --coverage \ | |
| --ci \ | |
| --profile github \ | |
| --changed-since HEAD^ | tee nf-test.txt | |
| - name: Add coverage reports | |
| if: ${{ github.event_name == 'pull_request' }} | |
| continue-on-error: true | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| bash .github/scripts/nftest_coverage_comment.sh nf-test.txt |