Important! Template update for nf-core/tools v3.3.1 #249
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Hi @mirpedrol, I think I fixed the tests as you meant (by loading the specific test profiles from the .nf.test files... |
mirpedrol
reviewed
Jun 17, 2025
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Thanks for taking over, @matbonfanti. I'm having trouble running the tests locally. I am wondering if the seed is correctly applied to the Bagel2 module. Were you able to verify this in your local test runs? |
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Hi yes, no problem, I am just about to re-run the tests locally, I tried with codespaces but I was not able to make it work (I have to admite I am quite inexperienced with it). Locally, I always seem to get the same results consistently, but I will do it another time and let you know... |
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Hi @mirpedrol , It is probably obvious at this point, but however I run the test locally I get always the same consistent md5sum (consistent with the current snapshot). I also checked the BAGEL command lines, when running the test both as a profile and as a nf-test test, and the command line is always:
so it seems that the seed argument is properly injected... I would like to actually compare the non-matching files, but I am not able to reproduce them in any way. Do you think you can give it a try with a codespaces instance? |
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I have tried to run the tests on Gitpod and they pass there. I will try to modify the GitHub action to upload the output files and be able to inspect them. |
Member
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Needs some polishing as the upload of the artifact is failing some times, but we can already see the files for one of the failing tests. |
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great, thanks! I will check the output files and let you know... |
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It looks like the difference comes from rows with identical log fold change (or another sorting key) being ordered differently. To avoid similar issues in the future, I suggest I take some time to trace the code generating these files and see if I can enforce a consistent and stable row ordering. I am very busy now. If you do not mind, I can give this a try next week. |
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Good investigation work! 🔍 |
…sprseq into nf-core-template-merge-3.3.1 * 'nf-core-template-merge-3.3.1' of github.com:nf-core/crisprseq: pass NXF_VER as input to use it for artifact name use github.run_id for artifact name add NF veresion to artifact name fix artifact path update glob pattern upload nf-test output as artifact skip modules and subworkflows nf-tests
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Hi @mirpedrol, However, the 58c58
< GTF3C1 -3.55 1 -1.97 0.0247 57 0.921 0.975 3420 0.99
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> GTF3C1 -3.55 1 -1.96 0.0247 57 0.921 0.975 3420 0.99This appears to be caused by some floating-point instability in the underlying arithmetic. IMHO, debugging this in detail might require substantial effort and is likely beyond the scope of standard pipeline maintenance. Let me know your thoughts. |
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that's great! Sounds good, I agree it's better to ignore md5 for unstable files and only check the presence of the file |
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finally! seems that we can finally merge the code... Do you think we can keep the changes that you made for keeping the test outputs as artifacts? it may come in handy in the future ;-) |
mirpedrol
approved these changes
Jun 26, 2025
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mirpedrol
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Yes, we should keep them! Let's add a comment to take it into account on future template merges, because I think this will generate merge conflicts in the future
| echo "| ⚠️ | No test results found | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY | ||
| fi | ||
| - name: Upload nf-test output directory |
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Suggested change
| - name: Upload nf-test output directory | |
| # Keep this code when resolving merge conflicts. Was added for debugging of nf-test | |
| - name: Upload nf-test output directory |
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ops, I did not realize that I had to add the comment before merging, I thought it was already commited... my bad, I will add the comment directly to the dev branch
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Version
3.3.1of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the
nf-core-template-merge-3.3.1branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.
For more information about this release of nf-core/tools, please see the
v3.3.1release page.