Does multiqc somehow create less plots in the `mul...
# multiqcj
Jonas S
10/13/2025, 10:56 AMDoes multiqc somehow create less plots in the
multiqc_plotsp
Phil Ewels
10/13/2025, 11:06 AMI don't think that MultiQC knows or cares about Nextflow
Phil Ewels
10/13/2025, 11:07 AMI mean, multiqc ❤️ nextflow of course, don't want to hurt any software's feelings
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nextflow deal with it 1
Phil Ewels
10/13/2025, 11:07 AMBut MultiQC doesn't alter its behaviour in any way according to whether it is or isn't run within a Nextflow pipeline
j
Jonas S
10/13/2025, 11:27 AMThanks phil 😄 what I thought as well. Guess I’ll dig a bit more into it… this is fine fire
this is fine fire 1
p
Phil Ewels
10/13/2025, 12:09 PMActually looking at the CI logs now. Looks like new plots,
mass_error.{pdf,png,svg}scores_xcorr.{pdf,png,svg}Phil Ewels
10/13/2025, 12:10 PMThey are showing up as new in the CI logs for both versions of Nextflow though, so nf-test is throwing an error with Nextflow latest:
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FAILED (550.442s)
Assertion failed:
1 of 2 assertions failed
Nextflow stdout:
N E X T F L O W ~ version 25.04.8Phil Ewels
10/13/2025, 12:11 PMit's just that those CI jobs are showing as passed, when they should be failed. Which is... odd
Phil Ewels
10/13/2025, 12:11 PMLooks like it's the step that checks if nf-test failed, which is itself failing, which is causing the CI test to pass 😵💫
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Error: Test with latest-everything failed
Warning: Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing.aaahhhh 1
Phil Ewels
10/13/2025, 12:13 PMunclear why it failed, it looks fine 🤔
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if [[ "failure" == "failure" ]]; then
echo "::error::Test with latest-everything failed"
# Add to workflow summary
echo "## ❌ Test failed: docker | latest-everything | Shard 1/5" >> $GITHUB_STEP_SUMMARY
if [[ "latest-everything" == "latest-everything" ]]; then
echo "::warning::Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing."
fi
if [[ "latest-everything" != "latest-everything" ]]; then
exit 1
fi
fiPhil Ewels
10/13/2025, 12:13 PMohhh wait it's the
latest-everythinglatest-everything💥 1
Phil Ewels
10/13/2025, 12:13 PMSo that new edge releases can't take down all nf-core CI in one go without warning
Phil Ewels
10/13/2025, 12:14 PMOk so this makes sense to me now:
• Your pipeline added some new MultiQC plots
• All nf-test CI jobs failed
• The
latest-everythingPhil Ewels
10/13/2025, 12:15 PMWe should probably supplement this log message with a link to some docs:
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Warning: Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing.this 1
j
Jonas S
10/13/2025, 12:23 PMThanks for debugging! That makes sense then 🙏 Updating the snapshots should fix this. ACTUALLY if I have your attention now 😄 I would want to update snapshots with nf-core bot (see this PR). We could test this on pipeline level right away
p
Phil Ewels
10/13/2025, 12:24 PMoh nice! Yeah seems like a good test.
Phil Ewels
10/13/2025, 12:24 PMCan you start a new thread in #C069B2Z5P1R about this first please?
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Phil Ewels
10/13/2025, 12:25 PMI went on a huge wild-goose-chase trying to build this the other day (trying to be too clever and using snapshot files from past runs, was a failure). And Julia has also built other workflows specifically for GPU etc.
Phil Ewels
10/13/2025, 12:25 PMIt'd be good to get eyes on it quickly before we merge + test
🙌 1
Phil Ewels
10/13/2025, 12:25 PMIf it works I'd love to add it into the template. Might even get it in before this tools release if we're speedy.
Phil Ewels
10/13/2025, 12:25 PMIf you post I can ping fokls
j
Jonas S
10/13/2025, 12:30 PMPosted ✅
p
Phil Ewels
10/13/2025, 12:42 PMThanks!
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