Integration Tests #1148
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Integration Tests | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| workflow_run: | |
| workflows: ["Pull latest UShER Source"] | |
| branches: [ master ] | |
| types: | |
| - completed | |
| env: | |
| BUILD_TYPE: Release | |
| jobs: | |
| build: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Pull latest tree | |
| run: | | |
| wget ${{ secrets.GLOBAL_TREE_PATH }} | |
| ls | |
| - name: Checkout ShUShER | |
| uses: actions/checkout@v2 | |
| - name: Parse UShER Version | |
| run: echo "USHER_VERSION=$(cat ./usher_version.txt)" >> $GITHUB_ENV | |
| - name: Checkout UShER | |
| uses: actions/checkout@v2 | |
| with: | |
| repository: yatisht/usher | |
| ref: ${{ env.USHER_VERSION }} | |
| path: usher | |
| - name: Compile and run UShER (C++) | |
| working-directory: usher | |
| run: | | |
| sudo install/installUbuntu.sh | |
| wget https://hgwdev.gi.ucsc.edu/~angie/UShER_SARS-CoV-2/2021/01/20/public-2021-01-20.all.masked.pb.gz | |
| build/usher -k50 -i public-2021-01-20.all.masked.pb.gz -d . -v ../usher-port/test/preload/test_samples.vcf | |
| - name: Compile and run UShER (WebAssembly) | |
| working-directory: usher-port | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install wget python3 build-essential cmake protobuf-compiler dh-autoreconf | |
| ./installUbuntuWeb.sh test | |
| node --experimental-wasm-threads build/usher.js -k50 -i ../usher/public-2021-01-20.all.masked.pb.gz -T1 -d . -v test/preload/test_samples.vcf | |
| echo "DIFF_PASSED=1" >> $GITHUB_ENV | |
| cmp ../usher/final-tree.nh ./final-tree.nh || echo "DIFF_PASSED=0" >> $GITHUB_ENV | |
| cmp ../usher/mutation-paths.txt ./mutation-paths.txt || echo "DIFF_PASSED=0" >> $GITHUB_ENV | |
| - name: Check diffs | |
| if: ${{ env.DIFF_PASSED == 0 }} | |
| uses: actions/github-script@v3 | |
| with: | |
| script: | | |
| core.setFailed('The output files of UShER and ShUSHER do not match.') |