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Dockerfile tests and cleanup imputation/PRS (#202)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,96 @@ | ||
| name: Dockerfile tests | ||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| pull_request: | ||
| paths: | ||
| - '**/Dockerfile' | ||
| schedule: | ||
| - cron: '23 2 * * 0' | ||
| concurrency: | ||
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | ||
| cancel-in-progress: true | ||
| jobs: | ||
| define_changed_dockerfile_matrix: | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| matrix: ${{ steps.changed-dockerfiles.outputs.all_changed_files }} | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - | ||
| name: Get Changed Dockerfiles | ||
| id: changed-dockerfiles | ||
| uses: tj-actions/changed-files@v44 | ||
| with: | ||
| matrix: true | ||
| files: '**/Dockerfile' | ||
| files_ignore: '**/GlimpseImputationPipeline/glimpse_docker/Dockerfile' | ||
| - name: List dockerfiles | ||
| run: echo '${{ steps.changed-dockerfiles.outputs.all_changed_files}}' | ||
|
|
||
| define_all_dockerfile_matrix: | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| matrix: ${{ steps.all-dockerfiles.outputs.files}} | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - | ||
| name: Get all Dockerfiles | ||
| id: all-dockerfiles | ||
| run: | | ||
| { | ||
| echo 'files<<EOF' | ||
| find . -name "Dockerfile" ! -path "*/GlimpseImputationPipeline/glimpse_docker/*" | jq -R . | jq -s . | ||
| echo EOF | ||
| } >> "$GITHUB_OUTPUT" | ||
| - name: List dockerfiles | ||
| run: echo '${{ steps.all-dockerfiles.outputs.files}}' | ||
|
|
||
| test_builds: | ||
| runs-on: ubuntu-latest | ||
| needs: [define_changed_dockerfile_matrix, define_all_dockerfile_matrix] | ||
| strategy: | ||
| matrix: | ||
| dockerfile: ${{ github.ref != 'refs/heads/main' && fromJSON(needs.define_changed_dockerfile_matrix.outputs.matrix) || fromJSON(needs.define_all_dockerfile_matrix.outputs.matrix) }} | ||
| fail-fast: false | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - | ||
| name: Get context | ||
| id: get-context | ||
| run: | | ||
| echo "context=$(dirname ${{ matrix.dockerfile }})" >> $GITHUB_OUTPUT | ||
| - | ||
| name: Build | ||
| uses: docker/build-push-action@v6 | ||
| with: | ||
| context: ${{ steps.get-context.outputs.context }} | ||
| file: ${{ matrix.dockerfile }} | ||
|
|
||
| test_glimpse_docker: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - | ||
| name: Check if Dockerfile has changed | ||
| id: check-if-changed | ||
| if: ${{ github.ref != 'refs/heads/main' }} | ||
| uses: tj-actions/changed-files@v44 | ||
| with: | ||
| files: '**/GlimpseImputationPipeline/glimpse_docker/Dockerfile' | ||
| - | ||
| name: Build main GLIMPSE Docker | ||
| if: ${{ github.ref == 'refs/heads/main' || steps.check-if-changed.outputs.all_changed_files_count > 0 }} | ||
| run: | | ||
| cd GlimpseImputationPipeline/glimpse_docker | ||
| ./build_base_and_extension_docker.sh -r https://github.com/odelaneau/GLIMPSE.git -t test -b master -y | ||
| - | ||
| name: Build Extract Num Sites Docker | ||
| if: ${{ github.ref == 'refs/heads/main' || steps.check-if-changed.outputs.all_changed_files_count > 0 }} | ||
| run: | | ||
| cd GlimpseImputationPipeline/glimpse_docker | ||
| ./build_extract_num_sites_from_reference_chunk_docker.sh -y -r https://github.com/michaelgatzen/GLIMPSE.git -t test -b master | ||
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