test

.github/workflows/ci.yml

@@ -47,18 +47,34 @@ jobs:
         run: |
           nextflow secrets set NCBI_API_KEY ${{ secrets.NCBI_API_KEY }}
 
+      - 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/genomeassembly --revision ${{ steps.branch-names.outputs.current_branch }} --compress none -d --force --outdir sanger-genomeassembly --container-cache-utilisation amend --container-system singularity
+
       - name: Download test data
         run: |
           curl https://tolit.cog.sanger.ac.uk/test-data/resources/genomeassembly/genomeassembly_test_data.tar.gz | tar xzf -
 
       - name: Setup apptainer
         uses: eWaterCycle/setup-apptainer@main
 
-      - name: Set up Singularity
-        run: |
-          mkdir -p $NXF_SINGULARITY_CACHEDIR
-          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
-
       - name: Run pipeline with test data
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_github,singularity --outdir ./results