Julianus Pfeuffer
Julianus Pfeuffer
Using a fragment_tolerance of > 50 ppm will exactly use the parameters you described. In theory, you can overwrite parameters that are not available on the command line by providing...
I don't know. Where do we stop then? I think if users know about these special flags, they also can pass a config file. Let's wait if it works.
No one complained about this anymore, I guess the config approach is fine for 99% of the use cases.
No worries! Good to clear that up for other users.
Hi! The error is here: 1 | 1 | Margolis_Mouse_Neuronal_TMT_TP_F1.mzML | 8 | 8 -- | -- | -- | -- | -- 1 | 1 | Margolis_Mouse_Neuronal_TMT_TP_F1.mzML | 8...
The last files look fine to me. Did you make sure there are no leftovers of the old file cached somewhere? I am not sure how this behaves during a...
This tool is not merged into dev yet. I think you are building containers from dev only.
I merged it now. You still need new containers.
Hi! This is indeed not well thought out. I would vote for specifying it comma-separated in the SDRF (1.), then the DIANN steps should take care of combining them again....
I think CLI vs Json params is handled via nextflow and should be correctly reflected in the pipeline_info. Only params in the sdrf might overwrite them. Something to consider is...