A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Another silly question, why is `nf-core` looking in `modules/nf-core/nf-core`?
```CRITICAL Cannot find directory 'modules/nf-core/nf-core/nextclade/datasetget'. Should be TOOL/SUBTOOL or TOOL                                                                                        ```

I'm running:
```nf-core modules test```
Then entering in
```? Tool name: nf-core/nextclade/run```
On the prompt. I get this error:
```CRITICAL Cannot find directory 'modules/nf-core/nf-core/nextclade/run'. Should be TOOL/SUBTOOL or TOOL                                                                                               ```

When I run
```nf-core modules test --profile docker nextclade/run```
I get this error
```ERROR    Nothing to execute. Is the file 'main.nf.test' missing?                                                                                                                                     
CRITICAL Ran, but found errors:                                                                                                                                                                      
          - Nothing to execute. Is the file 'main.nf.test' missing?        ```

I've confirmed that `nextclade/run` exists:
```(nf-core) [!!!! amplicon-nf !!!!] % ls modules/nf-core/nextclade/run/
tests/  environment.yml  <http://main.nf|main.nf>  meta.yml```

```? Tool name: nf-core/nextclade/run```


I'm having trouble uploading screenshots but it auto fills:
```? Tool name: nextcl
                    nf-core/nextclade/run         
                    nf-core/nextclade/datasetget  ```

What tools version are you using? Are you running this from a clone of the modules repo?

I'm running this inside an nf-core pipeline where the modules were installed using `nf-core` tool.

Running `nf-core modules list local` works perfectly.

```│ nextclade/run        │ nf-core/modules │ 41dfa3f     │ update meta.yml of all modules (#8747)            │ 2025-07-07 │
│ samtools/coverage    │ nf-core/modules │ 41dfa3f     │ update meta.yml of all modules (#8747)            │ 2025-07-07 │```

Well yes, `nf-core modules test` is not intended for that use-case

Nor is it intended to really modify the module tests within pipelines

Riiight I follow, thank you for clarifying