Medhat

Thank you @jnothman that fixed the issue by using `mpl.rcParams['font.size'] = 15` It would be nice to implement it in UpSetPlot (if possible) With that said for option `show_counts='%d'` can...

Thank you!

Thank you @RenzoTale88 , Sure, you can control the number of threads; for aligning I refer you to this section: ``` # Aligner ######### aligner: "minimap" # minimap or ngmlr...

> Great thanks @MeHelmy. One more thing: if I limit `-j 1`, will I run one task at the time locally? Thank you again! Yes, the `J` option will make...

> @MeHelmy one minor note: I've tried to run the workflow on a single node of our cluster, submitted within a nextflow workflow. The process starts without issues, however it...

Sure! anytime, " It is quite interesting, because the nextflow job simply calls princess inside a bash script" -- Good point, I will remove it and test it on my...

Hi @Neato-Nick, Thank you for reaching, Princess works on either PacBio or Nanopore but not a combination of both. Because each technology has its own error model. So, combining them...

That is perfect. So, you can use both CLR and ONT. If you care only for variants, you can use `princess variant` option, which will call SNVs, indels, and SVs....

Right, So If you want to phase also SNVs, then you are on the right track by choosing `princess all`.

If you run each technology separately (which we discussed earlier) then "phasing the nanopore samples with the BacBio wouldn't actually improve the phasing overall right?" will not take place, because...