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I think this is a question related to nf-validatio...
# nextflow-plugins
a
I think this is a question related to nf-validation. I added a new parameter to my local version of Sarek and now I get this (unwanted) warning:
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WARN: The following invalid input values have been detected:

* --skip_ngc_hpc_config: false
I tried adding the new parameter (skip_ngc_hpc_config) to 
schema_ignore_params
and 
validationSchemaIgnoreParams
but that didn’t help.
n
Have you set a default in the 
nextflow.config
?
a
Yes,
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skip_ngc_hpc_config = false
as the very first statement in 
nextflow.config
.
n
eh I really need to take a thorough look at that part of the code but I don't have time for it right now 😁
it's probably something stupid again 😛
a
I suspect it’s something stupid on my side 😆
n
that's also possible 😁
is it inside a 
params
scope?
a
yes
I was thinking about adding that new parameter to 
nextflow_schema.json
- that would silence the warning, right?
n
Oh
yep
a
It’s still needs to be in the schema.
n
that's the issue
a
ah!
So in Sarek we have 
params.genomes
defined nextflow.config, but I don’t see 
genomes
defined in our nextflow_schema.json - is that as it should be? 🤔
n
yes that's a 
map
type which isn't supported by 
nf-validation
and 
nf-schema
for parameters 😛
so it's best to ignore this until it's been implemented
a
ok, guys. Thanks for the prompt answers 🤝 I might just have learn something here. (I’ll probably forget real fast 🙈 )
n
No problem, happens to the best of us 😉
a
N.B. Now that warning is gone 🙂
🎉 1
@Nicolas Vannieuwkerke : I got this:
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WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`
I see you worked on that here. What would a local quick-fix be?
n
You should set defaults for 
params.monochromeLogs
and 
params.monochrome_logs
I don't think there's anything else you can do about it in 
nf-validation
👍 1
a
ok, setting 
params.monochromeLogs
seems to have been enough.
n
Awesome!
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