https://nf-co.re logo
Join Slack
Powered by
<@U04UWPBRAFP> I tried to test PCA-task related ch...
# scdownstream
k
@Nico Trummer I tried to test PCA-task related changes with AI-suggested subworkflow-specific command 
nf-test test subworkflows/local/integrate/tests/main.nf.test
and it explained that there was an error: 
Unknown configuration profile: 'test'
> because nf-test.config contained the "test" profile, but configFile pointed to tests/nextflow.config, which doesn't contain the test profile. so it suggested to delete 
profile "test"
from the file 
nf-test.config
. It indeed resolved the problem, but I suspect that there might be consequences elsewhere...
Also after this nf-test command there are multiple env-related issues with test cases on bbknn, combat, harmony like this:
Copy code
Command error:
    Traceback (most recent call last):
      File ".command.sh", line 5, in <module>
        from threadpoolctl import threadpool_limits
    ModuleNotFoundError: No module named 'threadpoolctl'
m
I would recommend to run:
Copy code
nf-test test --profile=+docker ...
👀 1
profile test should only be coming from the main root nextflow.config
🎓 1
and running via --profile=+docker will only append docker (or whatever you prefer) to the configs you have specified in the tests
k
@Maxime Garcia thank you, this worked!
m
🙏
2 Views
Open in Slack
PreviousNext
Powered by