Update memory needs #83
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| name: nf-core CI | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| release: | |
| types: [published] | |
| # Uncomment if we need an edge release of Nextflow again | |
| # env: NXF_EDGE: 1 | |
| jobs: | |
| test: | |
| name: Run workflow tests | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'GuilleGorines/PikaVirus') }} | |
| runs-on: ubuntu-latest | |
| env: | |
| NXF_VER: ${{ matrix.nxf_ver }} | |
| NXF_ANSI_LOG: false | |
| strategy: | |
| matrix: | |
| # Nextflow versions: check pipeline minimum and current latest | |
| nxf_ver: ['20.04.0', ''] | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Check if Dockerfile or Conda environment changed | |
| uses: technote-space/get-diff-action@v4 | |
| with: | |
| FILES: | | |
| Dockerfile | |
| environment.yml | |
| - name: Build new docker image | |
| # if: env.MATCHED_FILES | |
| run: docker build --no-cache . -t pikavirus:dev | |
| # - name: Pull docker image | |
| # if: ${{ !env.MATCHED_FILES }} | |
| # run: | | |
| # docker pull pikavirus:dev | |
| #docker tag pikavirus:dev guillegorines:pikavirus:dev | |
| - name: Install Nextflow | |
| env: | |
| CAPSULE_LOG: none | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline with test data | |
| # TODO nf-core: You can customise CI pipeline run tests as required | |
| # For example: adding multiple test runs with different parameters | |
| # Remember that you can parallelise this by using strategy.matrix | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE}/main.nf -profile test,docker |