https://nf-co.re logo
Join Slack
Powered by
So what's up with the standard profile? I thought ...
# nostupidquestions
s
So what's up with the standard profile? I thought that based on this text in the docs:
Copy code
When you do not specify a profile, Nextflow uses the standard profile by default.
That the standard profile would only be applied in the absence of other profiles (or when selecting it directly) but it seems to always be applied regardless of other profiles in my testing....
n
I think the "standard profile" is 
base
in nf-core and it is what sets all defaults, and the deafults apply unless changed by a different profile
I think most nf-core pipelines have 
includeProfile 'conf/base.config'
somewhere in their 
nextflow.config
But maybe you are not talking about nf-core but about nextflow more broadly?
s
That's not quite what I'm talking about, see here https://www.nextflow.io/docs/latest/config.html#config-profiles
but yes I am talking about nextflow broadly
I think this is the block which is responsible, I'm not sure if this is enough to justify a bug but I guess the behaviour does contradict the documentation
n
Very strictly reading, the documentation does not say what happens when you specify a profile, but I think it would be good to make it clearer
s
Ooops I was actually wrong, I had forgotten I had some system level config file which was applying the same
3 Views
Open in Slack
PreviousNext
Powered by