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<#C07URFZF074|> green on the new strict Nextflow s...
# proteinfamilies
e
🙌🏻 1
🎉 2
🙌 1
p
Awesome! 👏🏻
Nearly there - to get true green status ✅ you need to get it to run 
--help
with strict syntax enabled
looks like it'll be a case of updating nf-schema to fix the "unrecognised config option" thing
e
Oh so that was what Famke was doing
p
and updating the utils subworkflow to fix the "param true" thing (I already fixed that in the subworkflow)
hopefully it's basically one CLI command and one character change
e
Is it like this PR: https://github.com/nf-core/variantprioritization/pull/56/changes or is this something else?
except if you mean to just run 
nf-core subowrkflows update
After the update:
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WARN: Unrecognized config option 'validation.defaultIgnoreParams'
WARN: Unrecognized config option 'validation.monochromeLogs'
A workflow named 'UTILS_NFSCHEMA_PLUGIN' is already defined or included in script: /home/vangelis/Desktop/Projects/proteinfamilies/proteinfamilies/subworkflows/local/utils_nfcore_proteinfamilies_pipeline/main.nf
p
Ah if you have a local modified version then yeah you need fix that directly instead of updating / installing the shared one
And looks like you didn't update nf-schema?
From the output
e
I did try with the update (thats where the error above comes from) but havent pushed yet. Will have a look tomorrow!
p
You updated nf-schema version in the nf-test config, but not the pipeline config
e
The --help command still prints this line:
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A workflow named 'UTILS_NFSCHEMA_PLUGIN' is already defined or included in script: /home/path/to/proteinfamilies/subworkflows/local/utils_nfcore_proteinfamilies_pipeline/main.nf
Will 
UTILS_NFSCHEMA_PLUGIN
get removed from the next template update and be sourced only through the nf-schema plugin?
p
I don't think I got that error. Is that from my PR directly, or after you worked on it? It sounds like you ran 
nf-core modules install
to get the updates but actually you already had a local version of that subworkflow, so you ended up with two or something.
The subworkflow is still in the template for now, though Maxime wants to remove it and handle it with a plugin soon(ish) I think
Many people seem to have local versions of it in their pipeline though, with varying degrees of customisation
e
I pulled your branch and only added the latest git_sha number for the utils_nfschema_plugin subworkflow because it wouldn't match
p
if it's local then it shouldn't be mentioned in 
modules.json
at all
e
I am using the nf-core one, it's not local
p
wait I'm so confused 🙈 😆
sorry just looking at the PR again now, yes it's not local. Sorry, getting my wires crossed with too many pipelines
e
image.png
Also, this is still red locally: 😛
syntax error: 
Plugin 'nf-schema' does not exist or is not specified in the configuration file
p
I just cloned the repo again, checked out my branch and ran 
NXF_SYNTAX_PARSER=v2 nextflow run . --help
and I got no errors
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❯ nextflow -v
nextflow version 25.12.0-edge.0
e
I am on nextflow version 25.10.2.10555
25.10.3 is out, should I update? (I did, same printed line)
No biggie, I'll just merge your branch to dev and see if it goes green next 😄
p
yeah, having two versions of the same subworkflow seems wrong
you should either have a local copy or the shared version, not both
e
I don't have a local one!
p
blaaah can't read
was looking at your screenshot above and thought it was there twice
but it's a different subworkflow that's importing it
e
it's just included 😄
p
multyitasking too much, currently sat in the passenger seat of a driving car 😆
e
Can you trigger the test now that it's merged to dev?
Then your job is to select the music, dont do nextflow 😛
😅 1
p
Yeah ok, it's a Nextflow version thing - if I run with 
25.10.2
then I get the same errors as you
But 
25.12.0-edge
is fine
🎉 1
• ✅ 25.10.2 normal • ❌ 25.10.2 with 
NXF_SYNTAX_PARSER=v2
• ✅ 25.12.0-edge • ✅ 25.12.0-edge with 
NXF_SYNTAX_PARSER=v2
So I think we're fine - I can't see a reason for people to be using older versions of Nextflow and forcing strict syntax on
e
Nice..! Still doesn't work for the new ver 25.10.3 though
this 1
p
..with strict syntax enabled? yeah
that figures, as it's just backporting fixes to the previous stable.
I'll ask Ben about whether we should be also backporting fixes to the language parser, but because it's opt-in for those versions and not default, I'm not sure that it's worth it
That's kind of what I meant with my comment above - I mostly care about the default behaviour for different versions, so as long as it works by default with 25.10 (old parser) and 26.04 (new parser) then I'm fairly happy
You basically have to go out of your way to make it fail by using an old version of nextflow and feature flagging a new feature, which seems an unlikely thing for people to do
but still.. maybe we can backport some fixes in a 25.10.4 if it trips enough people up
e
Right! Gotcha!
Thanks 😄
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