Anyone know why the tests here pass when they shouldn't? https://github.com/nf-core/modules/pull/11072 The module has it's inputs changed, but for some reason the affected nf-tests which use the module in setup pass fine without the inputs being updated.

So we really are going with output suffix as an input value?

At least to me, it's better than ext.suffix. A pipeline user cannot mess with it unless permitted. It's controlled by the pipeline developer and the suffix is explicit in the process call instead of hidden in some config file under a bunch of

includeConfig

I see your point

│ WARN: Unknown directive

params

for process

GNU_SORT

│

│ WARN: Input tuple does not match tuple declaration in process

GNU_SORT

-- offending value: [[id:gtf], /nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.gtf] │

So it seems

tuple

cardinality mismatches are only warnings and not errors.

Iep, but the output of the tests should have been different, no?

No, the outputs should still be the same unless something else happened, like they were using the wrong config, etc

Yeah, so failing tests are still failing

These things aren't caught sometimes so the tests pass

I think we should do this on the script we're modifying on the PRs

Why not add it to the nf-test.config so it applies to all?

@Louis Le Nézet I have a feeling you're the person to ask about that

I think there's two things. Strict linting, and this other strict, and modules were converted for the strict syntax

Normally the whole modules repository is now nextflow strict syntax compliant. But I only tested it with 25.04.

I also had a bunch of sub-workflows / pipelines where I was passing the wrong number of argument, and nothing told me so until I ran the pipeline. Like @Mahesh Binzer-Panchal I though the original

strict

flag would be turned on by default in recent Nextflow but it isn’t, or would be embedded in the strict linter, but it isn’t either, and the flag is in fact deprecated.

That's what I find out this morning. The

nextflow.enable.strict

flag for running the test would have been nice to implement in the test.

Let's add it in for now https://github.com/nf-core/modules/pull/11089