Replace Github environment usage in Download Action #3351
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nf_core/pipeline-template/.github/workflows/download_pipeline.yml:32
- The raw tag '{% raw %}' seems out of place and might cause unintended behavior. It should be removed or corrected.
runs-on: ubuntu-latest{% raw %}
nf_core/pipeline-template/.github/workflows/download_pipeline.yml:38
- The raw tag '{% endraw %}' seems out of place and might cause unintended behavior. It should be removed or corrected.
- name: Install Nextflow{% endraw %}
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☝🏻 💩 |
mashehu
approved these changes
Dec 12, 2024
| echo "{% raw %}REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} | ||
| echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" | ||
| echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" | ||
| echo "{% raw %}REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" |
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| echo "{% raw %}REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" | |
| echo "{% raw %}REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"{% endraw %} |
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| - name: Run the downloaded pipeline (stub) | ||
| id: stub_run_pipeline | ||
| continue-on-error: true | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ./singularity_container_images | ||
| NXF_SINGULARITY_HOME_MOUNT: true | ||
| run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results | ||
| run: nextflow run ./${{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() }} |
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| if: ${{ job.steps.stub_run_pipeline.status == failure() }} | |
| if: ${{ steps.stub_run_pipeline.outcome == 'failure' }} |
According to the docs job context has status, but not steps
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According to the new GitHub Actions documentation,
$GITHUB_OUTPUTinstead of the environment should be used now to pass around values between steps and jobs.PR checklist
CHANGELOG.mdis updateddocsis updated