Update clean_fasta_cdna_cds.py #63
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| name: Docker Image CI | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| release: | |
| type: [published] | |
| env: | |
| TEST_TAG: dessimozlab/read2tree:test | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - | |
| name: Checkout | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: recursive | |
| - | |
| name: Docker meta | |
| id: meta | |
| uses: docker/metadata-action@v4 | |
| with: | |
| # list of Docker images to use as base name for tags | |
| images: | | |
| dessimozlab/read2tree | |
| # generate Docker tags based on the following events/attributes | |
| tags: | | |
| type=schedule | |
| type=ref,event=branch | |
| type=ref,event=pr | |
| type=semver,pattern={{version}} | |
| type=semver,pattern={{major}}.{{minor}} | |
| type=semver,pattern={{major}} | |
| type=sha | |
| - | |
| name: Set up QEMU | |
| uses: docker/setup-qemu-action@v2 | |
| - | |
| name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - | |
| name: Build and export to docker for testing | |
| uses: docker/build-push-action@v3 | |
| with: | |
| context: . | |
| load: true | |
| tags: ${{ env.TEST_TAG }} | |
| - | |
| name: Test | |
| run: | | |
| docker run --rm -i -v $PWD/tests:/input -v $PWD/tests/:/reads -v $PWD/output:/out -v $PWD/run:/run ${{ env.TEST_TAG }} --tree --standalone_path /input/marker_genes --dna_reference /input/dna_ref.fa --reads /reads/sample_1.fastq --output_path /out | |
| if [ ! -f output/tree_sample_1.nwk ] ; then exit 1; fi | |
| - | |
| name: Login to DockerHub | |
| if: github.event_name != 'pull_request' && github.event_name != 'push' | |
| uses: docker/login-action@v2 | |
| with: | |
| username: ${{ secrets.DOCKER_HUB_USERNAME }} | |
| password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }} | |
| - | |
| name: Build and push | |
| uses: docker/build-push-action@v3 | |
| with: | |
| context: . | |
| platforms: linux/amd64 | |
| push: ${{ github.event_name != 'push' && github.event_name != 'pull_request' }} | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} |