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Apply suggestions from code review
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Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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MatthiasZepper and mashehu authored Dec 13, 2024
1 parent 62ebfc1 commit 060eff5
Showing 1 changed file with 2 additions and 2 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ jobs:
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"
echo "{% raw %}REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"{% endraw %}
- name: Make a cache directory for the container images
run: |
Expand Down Expand Up @@ -103,7 +103,7 @@ jobs:
run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
- name: Run the downloaded pipeline (stub run not supported)
id: run_pipeline
if: ${{ job.steps.stub_run_pipeline.status == failure() }}
if: ${{ steps.stub_run_pipeline.outcome == 'failure' }}
env:
NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
NXF_SINGULARITY_HOME_MOUNT: true
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