Use gzip instead of pigz for kraken2 output compression #114
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| name: Build containers | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - develop | |
| # Do the builds on all pull requests (to test them) | |
| #pull_request: [] | |
| jobs: | |
| build-test-containers: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| # Keep going on other deployments if anything bloops | |
| fail-fast: false | |
| matrix: | |
| singularity_version: | |
| - '3.8.1' | |
| recipe: | |
| - "workflow/envs/Singularity.biobakery" | |
| - "workflow/envs/Singularity.krakenuniq" | |
| - "workflow/envs/Singularity.snakemake" | |
| - "workflow/envs/Singularity.stag-mwc" | |
| container: | |
| image: quay.io/singularity/singularity:v${{ matrix.singularity_version }} | |
| options: --privileged | |
| name: Check ${{ matrix.recipe }} | |
| steps: | |
| - name: Check out code for the container builds | |
| uses: actions/checkout@v3 | |
| - name: Continue if Singularity Recipe exists | |
| run: | | |
| if [[ -f "${{ matrix.recipe }}" ]]; then | |
| echo "keepgoing=true" >> $GITHUB_ENV | |
| fi | |
| - name: Build Container | |
| if: ${{ env.keepgoing == 'true' }} | |
| env: | |
| recipe: ${{ matrix.recipe }} | |
| run: | | |
| ls | |
| if [ -f "${{ matrix.recipe }}" ]; then | |
| sudo -E singularity build container.sif ${{ matrix.recipe }} | |
| tag=$(basename "${recipe/Singularity\./}-${GITHUB_REF_NAME}") | |
| # Build the container and name by tag | |
| echo "Tag is $tag." | |
| echo "tag=$tag" >> $GITHUB_ENV | |
| else | |
| echo "${{ matrix.recipe }} is not found." | |
| echo "Present working directory: $PWD" | |
| ls | |
| fi | |
| - name: Login and Deploy Container | |
| if: (github.event_name != 'pull_request') | |
| env: | |
| keepgoing: ${{ env.keepgoing }} | |
| run: | | |
| if [[ "${keepgoing}" == "true" ]]; then | |
| echo ${{ secrets.GITHUB_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io | |
| singularity push container.sif oras://ghcr.io/${GITHUB_REPOSITORY}:${tag} | |
| fi |