Test fix for downloading

nf-core · Jan 9, 2025 · e35d04f · e35d04f
1 parent e71095e
commit e35d04f
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Showing 2 changed files with 22 additions and 18 deletions.
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
@@ -29,11 +29,22 @@ env:
 
 jobs:
   configure:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-latest{% raw %}
     outputs:
       REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }}
       REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }}
       REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }}
+    steps:
+      - name: Get the repository name and current branch
+        id: get_repo_properties
+        run: |
+          echo "REPO_LOWERCASE=${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
@@ -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 "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 ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}
+        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}{% endraw %}{% if test_config %}{% raw %}
+
+      - name: Inspect container images
+        run: tree ./singularity_container_images | tee ./container_initial
 
       - name: Count the downloaded number of container images
         id: count_initial
@@ -123,8 +126,9 @@ 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!"
-          fi
+          fi{% endraw %}{% endif %}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,12 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.2.2 - Bouncy Basenji Patch [2024-12-20]
+## v1.2.2 - Bouncy Basenji Patch [2024-01-13]
 
 ### `Added`
 
 - [#558](https://github.com/nf-core/taxprofiler/pull/558) Updated to nf-core pipeline template v3.1.0 (added by @LilyAnderssonLee)
-- [#565](https://github.com/nf-core/taxprofiler/pull/565) Update to nf-core pipeline template v3.1.1 (added by @LilyAnderssonLee)
+- [#565](https://github.com/nf-core/taxprofiler/pull/565) Updated to nf-core pipeline template v3.1.1 (added by @LilyAnderssonLee)
 
 ### `Fixed`