Merge pull request #3389 from MatthiasZepper/no_env_in_download_action

Pipeline template: Fix the faulty Download test / GitHub action
nf-core · Jan 13, 2025 · 65969d9 · 65969d9
2 parents f58510f + 737b515
commit 65969d9
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,7 @@
 ### Download
 
 - Allow `nf-core pipelines download -r` to download commits ([#3374](https://github.com/nf-core/tools/pull/3374))
+- Fix faulty Download Test Action to ensure that setup and test run as one job and on the same runner ([#3389](https://github.com/nf-core/tools/pull/3389))
 
 ### Linting
 

diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml
@@ -35,7 +35,18 @@ jobs:
       REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }}
       REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }}
     steps:
-      - name: Install Nextflow{% endraw %}
+      - name: Get the repository name and current branch
+        id: get_repo_properties
+        run: |
+          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
+          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
+          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT{% endraw %}"
+
+  download:
+    runs-on: ubuntu-latest
+    needs: configure
+    steps:
+      - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
       - name: Disk space cleanup
@@ -56,24 +67,13 @@ jobs:
           python -m pip install --upgrade pip
           pip install git+https://github.com/nf-core/tools.git@dev
 
-      - name: Get the repository name and current branch set as environment variable
-        id: get_repo_properties
-        run: |
-          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
-          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
-          echo "{% raw %}REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
-
       - name: Make a cache directory for the container images
         run: |
           mkdir -p ./singularity_container_images
 
-  download:
-    runs-on: ubuntu-latest
-    needs: configure
-    steps:
       - name: Download the pipeline
         env:
-          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images{% raw %}
         run: |
           nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \
           --revision ${{ needs.configure.outputs.REPO_BRANCH }} \
@@ -85,7 +85,10 @@ jobs:
           --download-configuration 'yes'
 
       - name: Inspect download
-        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}{% endraw %}{% if test_config %}{% raw %}
+        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}{% endraw %}
+
+      - name: Inspect container images
+        run: tree ./singularity_container_images | tee ./container_initial{% if test_config %}{% raw %}
 
       - name: Count the downloaded number of container images
         id: count_initial
@@ -123,7 +126,8 @@ jobs:
             final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}
             difference=$((final_count - initial_count))
             echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
-            tree ./singularity_container_images
+            tree ./singularity_container_images > ./container_afterwards
+            diff ./container_initial ./container_afterwards
             exit 1
           else
             echo "The pipeline can be downloaded successfully!"