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CLI parameter case normalization/translation (kebab-case to camelCase) doesn't work at all since recent update #5655

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mhoban opened this issue Jan 8, 2025 · 2 comments · May be fixed by #5661
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@mhoban
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mhoban commented Jan 8, 2025

Bug report

Expected behavior and actual behavior

According to the documentation (and functionality in previous versions), nextflow should translate --kebab-case parameters into camelCase. There were some problems with this that I reported previously, which are stated to have been fixed in #4702, but now I'm not able to get it to work at all. In the version I'm using (24.11.0-edge build 5929), nothing at all happens when I pass --kebab-case parameters.

Steps to reproduce the problem

Here is a very simple workflow:

params.thingOne = "nothing"
workflow {
  println(params)
  println(params.thingOne)
}

When I do this:

nextflow run test.nf --thing-one newval

I would expect to see this output (according to #4702):

[thingOne:newval]
newval

But instead I see this:

[thing-one:newval, thingOne:nothing]
nothing

This actually appears to be a step backward from where we were before, because case translation worked then (despite other issues I may have had).

Program output

see above

Environment

  • Nextflow version: 24.11.0-edge build 5929
  • Java version: openjdk 17.0.5 2022-10-18
  • Operating system: Ubuntu 22.04.1 LTS (also tried on mac)
  • Bash version: GNU bash, version 5.1.16(1)-release (x86_64-pc-linux-gnu)
@mhoban
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mhoban commented Jan 8, 2025

I checked and can confirm that case translation works properly (in the pre-#4702 sense) in 24.08.0-edge, and does not work in 24.09.0-edge.

@bentsherman
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Thanks for reporting. That's a classic case of unit tests passing but no integration test 😅

I'll draft a fix shortly.

@bentsherman bentsherman linked a pull request Jan 9, 2025 that will close this issue
@bentsherman bentsherman added the bug label Jan 9, 2025
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