And another question:

pipelines lint

tells me that my local subworkflows have issues. However, I am somehow unable to get

subworkflows lint

to also check my local subworkflows, i tried

nf-core subworkflows lint <subworkflowname>

,

nf-core subworkflows lint local/<subworkflowname>

and

nf-core subworkflows lint subworkflows/local/<subworkflowname>

try

nf-core subworkflows lint <subworkflowname> --local

also does not work;

nf-core subworkflows lint assemble --local
ERROR    Could not find the specified subworkflow: 'assemble'

the subworkflow should be there:

ls subworkflows/local | head -n1
assemble

hmm, just tested and

subworkflows lint --local

lints all

<http://main.nf|main.nf>

in

subworkflows/local

interesting, I will take another look

just to be sure, can you check

subworkflows lint --local -passed

I will check that in a second, since I just wrote subworkflows, and did not make use of

subworkflows create

is it possible that this makes them not findable?

what is the structure of your local subworkflow?

Which brings me to my next question, is there some way to create a

meta.yml

for existing subworkflows?

very possible we miss it

it is

subworkflows/local/name/main.nf

to create a meta.yml, touch it and try with

lint --fix

or do you mean structure of the actual workflow?

you can check with

nf-core --verbose subworkflows lint --local

if it drops them for some reason

also

subworkflows lint --local

also only looks at local nf-core subworkflows

this was incorrect,

list local

only looks at local nf-core

yes, local here means: in this directory vs. in the modules repo

ok, so

subworkflows lint --local

does indeed lint all local subworkflows, but it does not seem to work with a named swf

what do you mean with "named subworkflows" exactly?

i mean that it works with

nf-core subworkflows lint --local

but not with

nf-core subworkflows lint <name> --local

ah, true. can you make an issue for that please?

Sure

I think local linting doesn't do fixes

Well, if I can just ignore the warnings about

meta.yml

that works for me 😉

They shouldn't lint by default in CI I don't believe, so really it's up to you what you choose to ignore. But maybe that was changed in the template at some point

I think it would be nice if they had meta.ymls, but I am not very keen on creating them manually