Faulty test command generated by create-test-yaml

[matthdsm]

Description of the bug

@drpatelh
First mentioned in nf-core/modules#1645 (comment)

generates:

command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c tests/config/nextflow.config

should be:

 command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config

Command used and terminal output

nf-core modules create-test-yml -f -p bowtie2/align

System information

nf-core v2.3.2

[drpatelh]

Appears like we need to update this line to reflect what we have in the module:

tools/nf_core/modules/test_yml_builder.py

Line 168 in e0d00d3

f"nextflow run tests/modules/{self.module_name} -entry {entry_point} -c tests/config/nextflow.config"

Not sure whether this happens when you have single/multiple tests to run.

[ewels]

- command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config

ok so we're missing a ./ (that bit shouldn't matter, right?) and missing a module-specific config file, gotcha 👍🏻

Not sure whether this happens when you have single/multiple tests to run.

I think you have to customise it with the CLI interactive prompt instead of using the default value in the code. Not sure what else we can do here.

[ewels]

-c ./tests/modules/bowtie2/align/nextflow.config - I don't think that this is needed. The workflow is in ./tests/modules/bowtie2/align so the nextflow.config in the same folder should be loaded automatically by Nextflow.

[matthdsm]

Actually, I've never had any issue. Like you said, the config is loaded automatically.
@drpatelh, what's the issue here exactly?

[ewels]

I think that the main reason was that the module-template should match the default command. I've put a draft PR together in #1568 where I (a) add the ./ prefix for clarity and to ensure it's local and (b) remove the unnecessary config load from the module template.

Not sure if this change will mean widespread changes are needed across nf-core/modules? 🤔 I think it's best to keep the commands as short as possible though.

[drpatelh]

There were issues but I can't remember now. Either way it would be good to be consistent with the syntax and for it to match the module template in tools because it makes it easier to update 100's of modules if everything looks the same. Had to do this before and it's not nice having to manually update things for consistency.

Maybe let's keep it as it is for now and we can deal with it later if required all in one go.

[ewels]

Maybe let's keep it as it is for now and we can deal with it later if required all in one go.

You mean keep the explicit -c in for now? Fine by me, shouldn't cause any issues and if removing it means manually updating tonnes of code then I see the attraction of keeping it 😅

Did we ever discuss a nf-core modules sync? 🤔

[ewels]

Added back in d61a51d