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Fix download tests #667

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Jan 20, 2025
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28 changes: 16 additions & 12 deletions .github/workflows/download_pipeline.yml
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,17 @@ jobs:
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"
download:
runs-on: ubuntu-latest
needs: configure
steps:
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
Expand All @@ -56,21 +67,10 @@ 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
Expand All @@ -87,6 +87,9 @@ jobs:
- name: Inspect download
run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}

- name: Inspect container images
run: tree ./singularity_container_images | tee ./container_initial

- name: Count the downloaded number of container images
id: count_initial
run: |
Expand Down Expand Up @@ -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!"
Expand Down
1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- Download tests [#667](https://github.com/nf-core/raredisease/pull/667)
- Restrict deepvariant analysis of WES samples to bait regions [#633](https://github.com/nf-core/raredisease/pull/633), [#658](https://github.com/nf-core/raredisease/pull/658)
- bcftools annotate declaration in annotate CADD subworkflow [#624](https://github.com/nf-core/raredisease/pull/624)
- Rhocallviz subworkflow will only be invocated once per sample [#621](https://github.com/nf-core/raredisease/pull/621)
Expand Down
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