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the tests for the config repo are failing due to s...
# configs
m
the tests for the config repo are failing due to strict syntax. anybody up for a quick fix? 👀 @Maxime Garcia @Nicolas Vannieuwkerke https://github.com/nf-core/configs/actions/runs/21977176720/job/63491317354
n
yeahhhhh this won't be a quick fix 😅
m
We should not use edge on this repo
that's my quick fix
n
But we should really start looking into fixing those
m
totally
but Matthias wanted a quick fix, I proposed one
m
but by using edge here, we catch things early. same as with tools. these tests are kind of nf-core canaries
m
true, but then it should be blocking PRs
similar to how we tests in pipeline
we know it fails in edge with strict syntax, but it's not there yet, so we have time to fix, and now the PRs are blocked
e
m
i update nf-test in the modules repo in the morning, might be related to that. @Nicolas Vannieuwkerke?
m
oh
no
why?
n
Might be a good idea to revert that for now, there seem to be some version mismatches between nf-test and the plugins
party this 1
m
there was a reason why we didn't push for that yet
nft-fastq is failing for now
we're working on it
m
I thought it was tested, sorry.
will revert
m
we should at least run a a test on a modules even when we don't change anything
m
m
that way we know we don't break things
m
i tested it locally with 0.9.4
n
I didn't test every plugin, I assumed since the ones I tested worked that there wouldn't be any problems 😁, well TIL
😁 1
m
but another case for an action that run's test for all modules 🙂
n
all plugins, you mean?
m
no, modules, that should then cover also most/all plugins 🙂
n
That's a massive action 😅
💯 1
m
a compromise? just test a handfull of configs with latest-everything https://github.com/nf-core/configs/pull/1012
n
How about running nextflow lint on them?
💯 1
m
good idea
m
I'd rather we run both a minimal NF version and latest everything on all, but only warn and not fails for latest everything
m
we have too many profiles to run both
m
do we really need to run them? or is linting sufficient?
m
let's try it just with linting then
👍 1
n
I took a look at trying to get the strict syntax to work on a config I use but it will require significant changes. We might want to push people to start updating these before it's too late
😬 1
👍🏻 1
m
m
but we still have issue when we run?
m
i guess so, because we didn't change anything in the configs. but i am back at using 25.04.8 (same as pipeline template)
m
oh
ok
m
actually if i run it manually i see errors. i will investigate
m
I'll try to have a look later then
for me we run only to make sure it works, so linting should have the same effect
but we would need latest-everything
n
My attempt at making our config compatible (untested but linting isn't complaining anymore for this one: https://github.com/nf-core/configs/pull/1013
👀 1
m
looking good
n
I still need to get it working though 😁
Okay it now works for both syntax parser versions
🚀 1
m
And you confirm that just running syntax is sufficient in that repo?
n
The main things to change are to move any 'unsupported' code in closures and call them with 
.call()
. Variables should be made parameters. I used the 
<config_name>_<variable_name>
for this, should be enough I think
Nextflow lint + the current tests should be enough
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