Improve caching behaviour for processes usingVALIDATOR outputs#619
Merged
atrigila merged 4 commits intonf-core:devfrom Jan 27, 2026
Merged
Improve caching behaviour for processes usingVALIDATOR outputs#619atrigila merged 4 commits intonf-core:devfrom
VALIDATOR outputs#619atrigila merged 4 commits intonf-core:devfrom
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grst
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Jan 23, 2026
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This works, and the runtime cost should be minimal since we are not dealing with huge data in differentialabundance.
Still would be curious what @pinin4fjords thinks of this approach:
tl;dr: Any change in the inputs causes VALIDATOR to run and invalidates the cache, even if it doesn't affect any downstream processes. Setting cache = deep on any process that consumes output of VALIDATOR solves this issue. For more details, see #520
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I'd add a comment to each of these entries to explain the why.
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This makes me a little nervous, we're assuming a lot about the size of the inputs future folks will apply, and the scale they'll be running at. I'd be more comfortable if this was implemented via a profile so folks would do |
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What I meant was that we are just operating on a fundamentally different scale in this pipeline, then, say, BAM files. I can live with the profile, but I think it would be a reasonable default if the caching just worked as expected, especially with large datasets. |
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Yes, but we're still significantly ramping up the overheads (even if from a very low base). How about a compromise, have it on by default, but give me a profile to turn it off and reset |
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ok, let's do that! Also, if you have any suggestion how to solve this differently, we are happy to give it a try! |
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I don't have a more cunning plan. The alternative might be to validate different things (matrices, contrasts) separately, but that has its own issues with complexity. This approach is reasonable. |
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@pinin4fjords @grst added the default profile and an explanation. |
pinin4fjords
approved these changes
Jan 27, 2026
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Closes #520
PR checklist
nf-core lint).nf-test test main.nf.test -profile test,docker).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).