Merge pull request #30 from sanger-tol/dp24_spelling #146
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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] | |
| env: | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Run pipeline with test data | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'sanger-tol/curationpretext') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "22.10.1" | |
| - "latest-everything" | |
| steps: | |
| - name: Get branch names | |
| # Pulls the names of current branches in repo | |
| # steps.branch-names.outputs.current_branch is used later and returns the name of the branch the PR is made FROM not to | |
| id: branch-names | |
| uses: tj-actions/branch-names@v8 | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Setup apptainer | |
| uses: eWaterCycle/setup-apptainer@main | |
| - name: Set up Singularity | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| - name: Install Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: Install nf-core | |
| run: | | |
| pip install nf-core | |
| - name: NF-Core Download - download singularity containers | |
| # Forcibly download repo on active branch and download SINGULARITY containers into the CACHE dir if not found | |
| # Must occur after singularity install or will crash trying to dl containers | |
| # Zip up this fresh download and run the checked out version | |
| run: | | |
| nf-core download sanger-tol/curationpretext --revision ${{ steps.branch-names.outputs.current_branch }} --compress none -d --force --outdir sanger-curationpretext --container-cache-utilisation amend --container-system singularity | |
| - name: Download test data | |
| # Download A fungal test data set that is full enough to show some real output. | |
| run: | | |
| curl https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData.tar.gz | tar xzf - | |
| - name: Singularity - Run ALL_FILES pipeline with test data | |
| # Remember that you can parallelise this by using strategy.matrix | |
| run: | | |
| nextflow run ./sanger-curationpretext/${{ steps.branch-names.outputs.current_branch }}/main.nf -profile test,singularity --outdir ./Sing-res |