Fix download pipeline workflow #470
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MatthiasZepper
approved these changes
Apr 12, 2024
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Fingers crossed that it works.
Admittedly, I have never thought about it which CI scripts are actually executed. Could well be that those from the default branch are used, which means one could fix as much as one wants on dev, until merged, the edits will not come into effect?
| uses: nf-core/setup-nextflow@v1 | ||
| uses: nf-core/setup-nextflow@v2 | ||
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| - name: Disk space cleanup |
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I do not know where the jlumbroso/free-disk-space step comes from. I have not heard of any issues with disk space so far, and it does uninstall a lot of packages that may or may not be needed. Probably no harm done here, but I believe also not strictly necessary.
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I will keep it in mind in case it causes issues in the future.
| NXF_SINGULARITY_CACHEDIR: ./ | ||
| NXF_SINGULARITY_HOME_MOUNT: true | ||
| run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results{% endraw %} | ||
| run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results |
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Exactly, that {% endraw %} did probably cause issues, because other than that you already have the most current version of the action with the fallback in case stub runs are not supported.
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PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).