Getting an odd linting error here the linter appears to imag nf-core #linting

Getting an odd linting error here - the linter app...

Jim Downie

03/19/2025, 1:09 PM

Getting an odd linting error here - the linter appears to imagine an extra output in one of the output tuples ("ap_ktab"):

Copy code

-- <http://main.nf|main.nf>
    output:
    tuple val(meta) , path("*${input_mat}.hap.ktab*", hidden: true), emit: mathap_ktab
    tuple val(meta2), path("*${input_pat}.hap.ktab*", hidden: true), emit: pathap_ktab
    path "versions.yml"                                            , emit: versions

-- linter error
Module meta.yml does not match <http://main.nf|main.nf>. Outputs should contain: {'mathap_ktab': ['meta', '${input_mat}.hap.ktab", hidden: true'], 'pathap_ktab': ['meta2', '${input_pat}.hap.ktab", hidden: true', 'ap_ktab'], 'versions': ['versions.yml']}

Is this a bug? https://github.com/nf-core/modules/pull/7847#issuecomment-2736500269

Simon Pearce

03/19/2025, 2:20 PM

Does it pass linting if you remove the "hidden: true"?

Simon Pearce

03/19/2025, 2:21 PM

Because I've never seen hidden: true in any other modules

Simon Pearce

03/19/2025, 2:22 PM

oh, three modules: https://github.com/search?q=repo%3Anf-core%2Fmodules%20hidden%3A%20true&type=code

Arthur

03/19/2025, 2:35 PM

I don't see an extra tuple listed in the expected outputs of that error message?

Jim Downie

03/19/2025, 2:36 PM

Dropping "hidden: true" from the meta.yml doesn't fix anything. Unfortunately it's needed in the module outputs as you need to emit

${prefix}.ktab

and

.${prefix}.ktab.1

Jim Downie

03/19/2025, 2:36 PM

@Arthur The linter says the expected output for the "pathap_ktab" is

pathap_ktab': ['meta2', '${input_pat}.hap.ktab", hidden: true', 'ap_ktab']

- there's an extra thing on the end there that shouldn't exist

Arthur

03/19/2025, 2:47 PM

Ok, I'm not sure where that extra bit is coming from, but there's a few inconsistencies in your meta.yml that you could try fixing first. • the output meta entries have a

pattern

which makes no sense • the output path entries have a trailing
"
but not a leading one, and it's not entirely obvious to me whether they should have the
hidden
part in the key like they do

Jim Downie

03/19/2025, 2:50 PM

The output pattern was generated when I ran

nf-core modules lint --fix

Arthur

03/19/2025, 2:52 PM

lol ok I worked out the issue

Arthur

03/19/2025, 2:53 PM

The way tools parses the outputs section, using a regex, if you have

path

(or

val/tuple

) in your emitted name, it breaks everything

🤣 1

Jim Downie

03/19/2025, 2:54 PM

oh my

Arthur

03/19/2025, 2:56 PM

There's not really a great fix for this I think. The required outputs are already ugly and borked because of

hidden

part too. Ideally we should rewrite nf-core linting to have a proper lexer and parser for the nextflow grammar such that we can better access the correct parts of the syntax. But it's possibly a lot of work and quite a bit slower than the current regex solution.

Jim Downie

03/19/2025, 2:56 PM

I'll rename the outputs to mat_hap_ktab and pat_hap_ktab for now - I presume that'll fix the regex issue

Arthur

03/19/2025, 2:57 PM

It should do yes

Jim Downie

03/19/2025, 3:01 PM

That's working now! Many thanks

Simon Pearce

03/19/2025, 3:03 PM

Can you make it look for

path(

path

mashehu

03/20/2025, 8:45 AM

it’s related to this bug I think https://github.com/nf-core/tools/issues/3483

👍 1

mashehu

03/20/2025, 8:45 AM

fix on the way

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