added option to read in masked positions as a file #181
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| name: "polyphonia CI" | |
| on: | |
| push: | |
| pull_request: | |
| branches: | |
| - master | |
| release: | |
| types: | |
| - created | |
| schedule: | |
| - cron: '0 18 * * 1' # weekly at 18:00 on Mondays | |
| env: | |
| HOME: "${{ github.workspace }}" | |
| CACHE_DIR: "${{ github.workspace }}/misc_cache" | |
| MINICONDA_DIR: "${{ github.workspace }}/miniconda" | |
| PYTHONIOENCODING: UTF8 | |
| GITHUB_ACTIONS_COMMIT: ${{ github.sha }} | |
| GITHUB_ACTIONS_BUILD_DIR: ${{ github.workspace }} | |
| GITHUB_ACTIONS_BRANCH: ${{ github.ref }} | |
| GITHUB_ACTIONS_PULL_REQUEST: ${{ github.event.number }} | |
| GITHUB_ACTIONS_PULL_REQUEST_BRANCH: ${{ github.head_ref }} | |
| GITHUB_ACTIONS_PULL_REQUEST_SHA : ${{ github.event.pull_request.head.sha }} | |
| GITHUB_ACTIONS_BASE_REF: ${{ github.base_ref }} | |
| DOCKER_REGISTRY: "quay.io" | |
| DOCKER_REPO_PROD: "quay.io/broadinstitute/polyphonia" | |
| DOCKER_REPO_DEV: "quay.io/broadinstitute/polyphonia" | |
| DOCKER_POLYPHONIA_PATH: "/opt/polyphonia" | |
| jobs: | |
| test_build_docker: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: checkout repository | |
| uses: actions/checkout@v2 | |
| - name: fetch tags | |
| run: git fetch --prune --unshallow --tags | |
| - name: Programmatic environment setup | |
| run: | | |
| set -e -x | |
| # $GITHUB_ENV is available for subsequent steps | |
| GITHUB_ACTIONS_TAG=$(git describe --tags --exact-match && sed 's/^v//g' || echo '') | |
| echo "GITHUB_ACTIONS_TAG=$GITHUB_ACTIONS_TAG" >> $GITHUB_ENV | |
| # | |
| # Set GITHUB_ACTIONS_BRANCH | |
| # TRAVIS_BRANCH: (via https://docs.travis-ci.com/user/environment-variables/ ) | |
| # for push builds, or builds not triggered by a pull request, this is the name of the branch. | |
| # for builds triggered by a pull request this is the name of the branch targeted by the pull request. | |
| # for builds triggered by a tag, this is the same as the name of the tag (TRAVIS_TAG). | |
| GITHUB_ACTIONS_BRANCH=$(git rev-parse --abbrev-ref HEAD) | |
| if [ -n "$GITHUB_ACTIONS_PULL_REQUEST_BRANCH" ]; then | |
| GITHUB_ACTIONS_BRANCH=${GITHUB_ACTIONS_BASE_REF##*/} | |
| elif [[ "${{ github.event_name }}" == "release" ]]; then | |
| GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_TAG | |
| fi | |
| echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV | |
| echo "GITHUB_ACTIONS_SHORT_SHA=$(echo $GITHUB_SHA | head -c8)" >> $GITHUB_ENV | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v1 | |
| - name: Cache Docker layers | |
| uses: actions/cache@v2 | |
| with: | |
| path: /tmp/.buildx-cache | |
| key: ${{ runner.os }}-buildx-${{ github.sha }} | |
| restore-keys: | | |
| ${{ runner.os }}-buildx- | |
| - name: Build and export | |
| id: docker_build | |
| uses: docker/build-push-action@v2 | |
| with: | |
| context: . | |
| push: false | |
| tags: "polyphonia:${{ env.GITHUB_ACTIONS_BRANCH }}-${{ env.GITHUB_ACTIONS_SHORT_SHA }}" | |
| cache-from: type=local,src=/tmp/.buildx-cache | |
| cache-to: type=local,dest=/tmp/.buildx-cache-new | |
| - name: Image digest | |
| run: echo ${{ steps.docker_build.outputs.digest }} | |
| # Temp fix | |
| # https://github.com/docker/build-push-action/issues/252 | |
| # https://github.com/moby/buildkit/issues/1896 | |
| - name: Store build in cache (overwrite) | |
| run: | | |
| rm -rf /tmp/.buildx-cache | |
| mv /tmp/.buildx-cache-new /tmp/.buildx-cache | |
| test_execution: | |
| runs-on: ubuntu-20.04 | |
| needs: test_build_docker | |
| steps: | |
| - name: checkout repository | |
| uses: actions/checkout@v2 | |
| - name: fetch tags | |
| run: git fetch --prune --unshallow --tags | |
| - name: Programmatic environment setup | |
| run: | | |
| set -e -x | |
| # $GITHUB_ENV is available for subsequent steps | |
| GITHUB_ACTIONS_TAG=$(git describe --tags --exact-match && sed 's/^v//g' || echo '') | |
| echo "GITHUB_ACTIONS_TAG=$GITHUB_ACTIONS_TAG" >> $GITHUB_ENV | |
| # | |
| # Set GITHUB_ACTIONS_BRANCH | |
| # TRAVIS_BRANCH: (via https://docs.travis-ci.com/user/environment-variables/ ) | |
| # for push builds, or builds not triggered by a pull request, this is the name of the branch. | |
| # for builds triggered by a pull request this is the name of the branch targeted by the pull request. | |
| # for builds triggered by a tag, this is the same as the name of the tag (TRAVIS_TAG). | |
| GITHUB_ACTIONS_BRANCH=$(git rev-parse --abbrev-ref HEAD) | |
| if [ -n "$GITHUB_ACTIONS_PULL_REQUEST_BRANCH" ]; then | |
| GITHUB_ACTIONS_BRANCH=${GITHUB_ACTIONS_BASE_REF##*/} | |
| elif [[ "${{ github.event_name }}" == "release" ]]; then | |
| GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_TAG | |
| fi | |
| echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV | |
| echo "GITHUB_ACTIONS_SHORT_SHA=$(echo $GITHUB_SHA | head -c8)" >> $GITHUB_ENV | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v1 | |
| - name: Cache Docker layers | |
| uses: actions/cache@v2 | |
| with: | |
| path: /tmp/.buildx-cache | |
| key: ${{ runner.os }}-buildx-${{ github.sha }} | |
| restore-keys: | | |
| ${{ runner.os }}-buildx- | |
| # re-build image (from cache; this seems faster than exporting the image and passing as an Actions artifact) | |
| - name: Build and export | |
| id: docker_build | |
| uses: docker/build-push-action@v2 | |
| with: | |
| context: . | |
| push: false | |
| load: true | |
| tags: "polyphonia:${{ env.GITHUB_ACTIONS_BRANCH }}-${{ env.GITHUB_ACTIONS_SHORT_SHA }}" | |
| cache-from: type=local,src=/tmp/.buildx-cache | |
| - name: Image digest | |
| run: echo ${{ steps.docker_build.outputs.digest }} | |
| - name: Create local dir for test output | |
| run: | | |
| mkdir -p output | |
| - name: Run polyphonia (basic execution test) | |
| run: | | |
| docker run -v $(pwd)/bin:${{ env.DOCKER_POLYPHONIA_PATH }} -v $(pwd)/test:${{ env.DOCKER_POLYPHONIA_PATH }}/test -v $(pwd)/output:/tmp/output --rm polyphonia:${{ env.GITHUB_ACTIONS_BRANCH }}-${{ env.GITHUB_ACTIONS_SHORT_SHA }} \ | |
| polyphonia cross_contamination | |
| - name: Run polyphonia (cross_contamination test) | |
| run: | | |
| set -e -x | |
| docker run -v $(pwd)/bin:${{ env.DOCKER_POLYPHONIA_PATH }} -v $(pwd)/test:${{ env.DOCKER_POLYPHONIA_PATH }}/test -v $(pwd)/output:/tmp/output --rm polyphonia:${{ env.GITHUB_ACTIONS_BRANCH }}-${{ env.GITHUB_ACTIONS_SHORT_SHA }} \ | |
| polyphonia cross_contamination \ | |
| --ref ${{ env.DOCKER_POLYPHONIA_PATH }}/test/input/NC_045512.2.fasta \ | |
| --vcf ${{ env.DOCKER_POLYPHONIA_PATH }}/test/input/USA-MA-Broad_CRSP-01315-2021.bam_LoFreq.vcf \ | |
| --vcf ${{ env.DOCKER_POLYPHONIA_PATH }}/test/input/USA-MA-Broad_CRSP-01323-2021.bam_LoFreq.vcf \ | |
| --consensus ${{ env.DOCKER_POLYPHONIA_PATH }}/test/input/USA-MA-Broad_CRSP-01315-2021.fasta \ | |
| --consensus ${{ env.DOCKER_POLYPHONIA_PATH }}/test/input/USA-MA-Broad_CRSP-01323-2021.fasta \ | |
| --plate-map ${{ env.DOCKER_POLYPHONIA_PATH }}/test/input/USA-MA-Broad_CRSP-01315_23-2021_plate_map.txt \ | |
| --min-depth 0 \ | |
| --output /tmp/output/potential_cross-contamination.txt \ | |
| --overwrite TRUE | |
| DIFF=$(diff $(pwd)/output/potential_cross-contamination.txt $(pwd)/test/output/potential_cross-contamination.txt) | |
| if [ "$DIFF" != "" ]; then | |
| echo "Failure: cross_contamination test output does not match expected output" | |
| echo " expected output:" | |
| cat $(pwd)/output/potential_cross-contamination.txt | |
| echo " test output:" | |
| cat ${{ env.DOCKER_POLYPHONIA_PATH }}/test/output/potential_cross-contamination.txt | |
| exit 1 | |
| else | |
| echo "Success: cross_contamination test" | |
| fi | |
| - name: Run polyphonia (cross_contamination test with aligned consensus sequences) | |
| run: | | |
| set -e -x | |
| docker run -v $(pwd)/bin:${{ env.DOCKER_POLYPHONIA_PATH }} -v $(pwd)/test:${{ env.DOCKER_POLYPHONIA_PATH }}/test -v $(pwd)/output:/tmp/output --rm polyphonia:${{ env.GITHUB_ACTIONS_BRANCH }}-${{ env.GITHUB_ACTIONS_SHORT_SHA }} \ | |
| polyphonia cross_contamination \ | |
| --ref ${{ env.DOCKER_POLYPHONIA_PATH }}/test/input/NC_045512.2.fasta \ | |
| --vcf ${{ env.DOCKER_POLYPHONIA_PATH }}/test/input/USA-MA-Broad_CRSP-01315-2021.bam_LoFreq.vcf \ | |
| --vcf ${{ env.DOCKER_POLYPHONIA_PATH }}/test/input/USA-MA-Broad_CRSP-01323-2021.bam_LoFreq.vcf \ | |
| --consensus-aligned ${{ env.DOCKER_POLYPHONIA_PATH }}/test/input/USA-MA-Broad_CRSP-01315_23-2021_MAFFT_aligned.fasta \ | |
| --plate-map ${{ env.DOCKER_POLYPHONIA_PATH }}/test/input/USA-MA-Broad_CRSP-01315_23-2021_plate_map.txt \ | |
| --min-depth 0 \ | |
| --output /tmp/output/potential_cross-contamination.txt \ | |
| --overwrite TRUE | |
| DIFF=$(diff $(pwd)/output/potential_cross-contamination.txt $(pwd)/test/output/potential_cross-contamination.txt) | |
| if [ "$DIFF" != "" ]; then | |
| echo "Failure: cross_contamination test output does not match expected output" | |
| echo " expected output:" | |
| cat $(pwd)/output/potential_cross-contamination.txt | |
| echo " test output:" | |
| cat ${{ env.DOCKER_POLYPHONIA_PATH }}/test/output/potential_cross-contamination.txt | |
| exit 1 | |
| else | |
| echo "Success: cross_contamination test" | |
| fi | |
| - name: Run polyphonia (cross_contamination test with aligned consensus sequences with gap in reference) | |
| run: | | |
| set -e -x | |
| docker run -v $(pwd)/bin:${{ env.DOCKER_POLYPHONIA_PATH }} -v $(pwd)/test:${{ env.DOCKER_POLYPHONIA_PATH }}/test -v $(pwd)/output:/tmp/output --rm polyphonia:${{ env.GITHUB_ACTIONS_BRANCH }}-${{ env.GITHUB_ACTIONS_SHORT_SHA }} \ | |
| polyphonia cross_contamination \ | |
| --ref ${{ env.DOCKER_POLYPHONIA_PATH }}/test/input/NC_045512.2.fasta \ | |
| --vcf ${{ env.DOCKER_POLYPHONIA_PATH }}/test/input/USA-MA-Broad_CRSP-01315-2021.bam_LoFreq.vcf \ | |
| --vcf ${{ env.DOCKER_POLYPHONIA_PATH }}/test/input/USA-MA-Broad_CRSP-01323-2021.bam_LoFreq.vcf \ | |
| --consensus-aligned ${{ env.DOCKER_POLYPHONIA_PATH }}/test/input/USA-MA-Broad_CRSP-01315_23-2021_MAFFT_aligned_gap_added.fasta \ | |
| --plate-map ${{ env.DOCKER_POLYPHONIA_PATH }}/test/input/USA-MA-Broad_CRSP-01315_23-2021_plate_map.txt \ | |
| --min-depth 0 \ | |
| --output /tmp/output/potential_cross-contamination.txt \ | |
| --overwrite TRUE | |
| DIFF=$(diff $(pwd)/output/potential_cross-contamination.txt $(pwd)/test/output/potential_cross-contamination.txt) | |
| if [ "$DIFF" != "" ]; then | |
| echo "Failure: cross_contamination test output does not match expected output" | |
| echo " expected output:" | |
| cat $(pwd)/output/potential_cross-contamination.txt | |
| echo " test output:" | |
| cat ${{ env.DOCKER_POLYPHONIA_PATH }}/test/output/potential_cross-contamination.txt | |
| exit 1 | |
| else | |
| echo "Success: cross_contamination test" | |
| fi | |