Bug: profile not recognized

[ggabernet]

Hi,

when using the Tower Launcher, a profile that is imported into nextflow.config is not recognized by the Tower launcher. In case this is relevant, the profile is defined in the dsl2 branch but not yet merged into the master branch.

https://github.com/nf-core/bcellmagic/blob/fba2622fefca465e351ed5e85f133863fca1303f/nextflow.config#L172

The profile does not appear in the drop-down menu:

And if trying to force it anyways, it fails to launch with this message:

[pditommaso]

I Gisella, I've tried with the new beta (here) and it looks the test_full is accepted, tho still not listed in the dropdown. @jordeu you may want to give a try, my understanding is that with the config parsed it should be detected .

[jordeu]

We have an error here, but it's not related with the parser it self. The problem is that only the profiles at master are used to do this checking, so given that test_full it's not at master and only at dsl2 branch this is why it complains with the unknown pipeline profile. We are going to fix this asap, but meanwhile if you want a workaround one option would be to create an empty test_full profile at master branch.

[ggabernet]

Ok thanks for checking it out!

[drpatelh]

Yep, I am seeing a similar thing and was a little confused too but it makes sense now if only the profile definitions on master are pulled in.

In my case, I was trying to use these two profile definitions that are only on the dev branch and not on master and so was unable to find them in the profile listing in Tower:

[pditommaso]

ok, currently the profile names are only taken from the master branch. It needs to be solved.