Hi nf-coder! I'm preparing the v2.0.0 of nf-core/isoseq pipeline. The code github action face an error at the linting step. I would be grateful if I can have assistance to solve this problem 🙂

the problem is the module name in the import statement I think: https://github.com/nf-core/isoseq/blob/dev/workflows/isoseq.nf#L59 should be

isoseq3/refine

It might be the origin of the problem indeed. However, isoseq3 is an older version. isoseq, without the 3, is the version 4.

ah, sorry, yes, correct

the older versions of nf-core/isoseq (version <2.0.0) still use isoseq3, so it can't remove I guess 😕

I think you are including

isoseq/refine

but the module in your pipeline is located under

isoseq3/refine

? and

isoseq3/refine

doesn't exist in nf-core

For being sure, I ran the commands you mentioned, but it's there's no error. There's no trace of isoseq3 😕 https://app.warp.dev/block/yw0Ewuex0phUK8gPZR7uk1 https://app.warp.dev/block/8SlCxhcedWvvuvo94mwPtd https://app.warp.dev/block/ojrIWwLzIT8pJjSDsHesxm

With the dev version of tools?

It's the version stable version:

nf-core/tools version 2.14.1

The modules repo uses the dev version

You think it can impact the linting of the pipeline?

do you have a link to the PR which is failing?

I didn't create the PR to master branch yet. The error is from the github actions triggered after a commit. I would like to fix tjis issue before opening the PR.

anywhere where I can see the code to debug?

I'm working on the dev branch of nf-core/isoseq. When I delete and recreate the

module.json

file. I have only two differences, on git_sha values for two

gstama

modules. I'm sure it's related to

isoseq/refine

.

I've been testing different things, I also tried installing the isoseq/refine module in the testpipeline, and tests pass. Your

modules.json

and module look fine. I am wondering if there is some cache and since the module name changed from isoseq3 to isoseq this is causing issues. Since the tests pass locally, could we try opening a PR and check if they pass there?

Same results with the pull request :/

I think I found the problem, this was a tricky edge case! Since the name of the pipeline and the module are the same, the linting command uses the wrong directory. This PR should fix it. But this won't be available for you rPR until the next tools release, one solution is to install the dev version in the github action, here

I'm so sorry for this problem 😅 I'm going to try the dev then.

oh true, this version includes big changes on the template. We could skip this linting for now but I think it will get confusing once v3.0.0 is out 🤔

So I changed back to the non dev version of nf-core tools and and applied your command. Now it complains about the linting.yml file which is not identical to the template.

you can add the following to the

.nf-core.yml

file to ignore this linting test

lint:
    files_unchanged:
        - ".github/workflows/linting.yml"

We have green! There's only the Editorconfig and Prettier tests that are still waiting. Maybe I should readd the -l option?

these are old test requirements that we don't have anymore, I can fix this in your repository settings

Thank you so much for all your help! I just need to polish and ask for reviews! 🙂

👏🏻 I'm glad it's solved!