Hi, I'm having issues getting the --help parameter...
# nf-schema
l
Hi, I'm having issues getting the --help parameter to work with my pipeline. Are there any limitations I should be aware of? I get this error: Parameter
help
was specified on the command line or params file but is not declared in the script or config Anyone know what this means? I followed the docs and am using nf-schema 2.6.1 and have validation { help { enabled = true } } In my config. The pipeline is quite large so it might be something else but am not sure what to look for. It started around the time I transitioned from NXF_VER=25.04.8 to 25.10.2
a
I think you still have to declare the
help
parameter in your
params
block. Certainly the
nf-core/tools
template still does. And the error you are getting I believe is coming from the
nextflow
strict syntax which I am guessing disallows undefined params being passed.
party this 1
l
That resolved my error, but --help still doesn't do anything 😞
a
Hmm, looking again at nf-core, we explicitly call
paramsHelp
. @Nicolas Vannieuwkerke are the docs for help out of date here?
n
The latest versions of nf-schema allow both help messages via the config options or via the function.
In nf-core we use the function for some fancy text before and after the message, but in most cases the configuration is fine
l
Ok, thank you, that minimal example really helps
extreme teamwork 1