Update StringTie to latest version

[rrdavis77]

Description of feature

Hello,

I just realized that StringTie had a major update to version 3.0.0 https://ccb.jhu.edu/software/stringtie/
It might be nice to update to this version during the next update to this great pipeline!

[SamCT]

Also very interested in this enhancement.
Particularly the nascent mode .

[pinin4fjords]

Major versions usually mean breaking changes- have you tried this as a drop-in replacement?

[rrdavis77]

Sorry Jonathan! I have not tried it as a drop-in replacement.

[QuyANgo]

I'm also particularly interested in the nascent mode.
It would be great to have StringTie v.3.0.0 updated for the pipeline.

[MatthiasZepper]

I'm also particularly interested in the nascent mode. It would be great to have StringTie v.3.0.0 updated for the pipeline.

The nf-core community always welcomes contributions, and the first step to make this happen would be to upgrade the StringTie modules.

There is always a technical and a scientific side to major version upgrades. The technical aspects are to ensure that the API has not changed in relevant ways: Are there new or different input files needed for V2 versus V3? Are there new output files? Did the CLI commands change, or the CLI parameter names?

The scientific part is the comparison of results on test datasets. If there is a publication for the new release, it could be that the examples and comparisons there suffice.

If you can help with any or all of these, you could clearly speed up the integration of the new version.