Hey all, I've recently added the `error_retry` lab...
# linting
f
Hey all, I've recently added the
error_retry
label to some of my modules. The heads of these modules look like this now:
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process FORCE_HIGHER_LEVEL {
    tag { tile }
    label 'process_medium'
    label 'error_retry'
When linting the pipeline, every module that has the
error_retry
label produces this warning:
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force-higher_level              │ modules/local/force-higher_level.nf             │ Non-standard labels found: error_retry
The
error_retry
is defined in the template's
base.config
file, so I assumed that it would be a standard label. Am I misunderstanding the usage of
error_retry
or is that a bug in
nf-core lint
?
s
which nf-core tools version is this ?
and do you have a branch that I can try myself ?
f
nf-core/tools version 2.14.1
Just pushed the changes to our fork: https://github.com/CRC-FONDA/nf-core-rangeland
s
nothing obviously wrong....one min...checking with another pipeline
👍🏻 1
don't see with methylseq....something must be off in this repo
f
no module in methylseq's master branch has the
error_retry
label. Adding a local module with the label to methylseq produces the same warning for me. Adding the label to a nf-core module does not produce the warning (but rather the error: "Local copy of module does not match remote") Seems to be related to local modules?
hmmm thats a good observation
could be specific to local modules
this could be a bug....could you raise an issue on tools gh ?
f
Yes, I will do that. Just confirming with some other pipelines.
👍 1
More observations: The warning only appears if the module is a single
.nf
file, e.g.
modules/local/force-mosaic.nf
It seems to be a standard that the modules are organized like this:
modules/local/force-mosaic/main.nf
Is the latter enforced by nf-core? The guidelines appear vague on that.
I see pipelines with official releases (e.g. mag ) that use the former structure, so I assume its not enforced.
s
not sure if we are enforcing it but, def recommend the latter structure
modules/local/force-mosaic/main.nf
as soon you will be expected to have a
tests/
sub-folder along with the main of each module
✅ 1