Hi I encountered the following issue when linting with the latest dev branch:

LookupError: Could not find branch information for component 'happy/happy/happy'.Please remove the 'modules.json' and rerun the command to recreate it

I already recreated the modules.json file but the error persists.

What lint command are you running, and which tools version?

nf-core pipelines lint

on the current dev branch 🙂

Hmm, any idea which of the lint tests is actually throwing the error?

This is the stacktrace

Same error?

snpeff/snpeff/snpeff

has no branch info?

yes

Ok so this is some weirdness where

<http://module.org|module.org>

must be being set to e.g.

snpeff

Yeah seems like such a thing, weird bug

And maybe it’s just coincidence, but seems odd that it happens so far with modules where

tool==subtool

yeah also true 🤔

Found the issue. It is indeed due to

tool==subtool

. https://github.com/nf-core/tools/blame/25224a03db8d16767e4241982f6bf66829a03b21/nf_core/components/nfcore_component.py#L67-L72 Looks like the guilty code went in 5 days ago so makes sense you see the error now

Nice that was fast!

@Nicolas Vannieuwkerke you missed a dad joke! Tools isn't happy because it can't find happy/happy/happy!

Love how you casually join the conversation to shame me into missing a dad joke 😉 (while casually dropping one yourself 🤣)

I'm running on very little sleep and trying to stop my son from killing himself, there is not much to live for at the moment

That explains the urge to drop some dad jokes 😉

The simplest fix (I think) is to apply a slightly different index search:

from operator import indexOf

def rindex(li, value):
    return len(li) - 1 - indexOf(reversed(li), value)

And then:

name_index = (
                len(self.component_dir.parts)
                - 1
                - rindex(self.component_dir.parts[::-1],self.component_name.split("/")[0])
            )

SCRATCH THAT: The current code is actually already reversing the list to find the index of the “last” occurrence of the component name. So actually we can just find the “first” using:

name_index = self.component_dir.parts.index(self.component_name.split("/")[0])

Caveat that I haven’t looked into why the changes were implemented in the first place so maybe something more needs to be done. @Júlia Mir may know.

do you have a code location for that? I'll try it out on my pipeline and see what it does

thanks

I think the issue is that Julia implemented this to handle the case where the

org==tool

maybe? And then my solution above also fails for the reverse reason

I'm currently looking into a possible fix that resolves both issues

Best thing I came up with off the top of my head is to split the directory as a string on the

component_name

then take the last element of it split by

/

. But it’s not very clean.

I already tried that but that isn't the issue (since in the bug's case the first and last element are the same)

Ok I have something which should work:

tool, subtool = self.component_name.partition("/")
    if subtool and (tool == subtool):
        idx = 1
    else:
        idx = 0
    
    name_idx = (
        len(self.component_dir.parts)
        - 1
        - self.component_dir.parts[::-1].index(tool, idx)
    )

(

.index

can take a starting or end idx to limit the search space to whilst still returning the actual index)

https://github.com/nf-core/tools/pull/3156 => with a very similar solution to yours

Reading this now! but I see you already found why I introduced the change 🕵🏻‍♂️ I'm not on my PC, but both of your solutions seem good, thanks for fixin it!

(it's failing for a changelog but nothing needs to be added to the changelog here 😛)