add keepalive api to keep repo active #263
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| on: | |
| pull_request: | |
| branches: | |
| - master | |
| push: | |
| branches: | |
| - GHactions_37d2b7a | |
| name: master Pull Request | |
| jobs: | |
| test: | |
| name: Run tests | |
| runs-on: ubuntu-latest | |
| env: | |
| NXF_ANSI_LOG: false | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: create artifacts dir to save test logs | |
| run: mkdir artifacts | |
| - name: install Singularity | |
| run: | | |
| bash .github/scripts/install_singularity.sh | |
| - name: Build pipeline Singularity containers | |
| run: | | |
| echo $(which singularity) | |
| bash scripts/build_singularity_containers.sh | |
| - name: install Conda | |
| run: bash .github/scripts/install_conda.sh | |
| - name: install Nextflow via Conda | |
| run: | | |
| export PATH=/opt/conda/bin:$PATH | |
| conda install -c bioconda nextflow | |
| NXF_VER=23.04.3 nextflow -version | |
| - name: test nanopore pipelines | |
| run: bash .github/scripts/test_nanopore_pipelines.sh | |
| - name: test typing functionality | |
| run: bash .github/scripts/test_typing.sh | |
| - name: test PR outputs against previous release | |
| run: bash .github/scripts/test_PR_against_release.sh | |
| - name: test -profile sanger | |
| run: bash .github/scripts/test_sanger_profile.sh | |
| - name: test --cache conda environment | |
| run: bash .github/scripts/test_conda_cache.sh | |
| - name: test --bed and --ref input options | |
| run: bash .github/scripts/test_bed_ref_input.sh | |
| - name: test --cram input together with --bed and --ref | |
| run: bash .github/scripts/test_cram_input.sh | |
| - name: test --outCram output together with --cram and --ref | |
| run: bash .github/scripts/test_cram_output.sh | |
| - name: if failure, add latest NF log to artifacts | |
| run: mv .nextflow.log artifacts/failure.nextflow.log | |
| if: failure() | |
| - uses: actions/upload-artifact@v1 | |
| if: always() | |
| with: | |
| name: test_artifacts | |
| path: artifacts |