General structure & "best practices"

[hoelzer]

Hey,

I am just looking at another small workflow that I think can yield as a nice example for some general structure and modularization changes:

https://github.com/replikation/MPOA

It does not have conda profile but this can be easily added. Then you will see the main nf file and the different workflows with their processes. I think that's a good general structure. Also the --help can be c&p and adjusted ;)

Of course there are more workflows with similar structure also from MF1, but that one is relatively small with only a few processes.

[hoelzer]

Here is a "mimimum viable example" from Marie which shows some "best practices". Just to note, actually I would define the conda/docker dependencies in separate configs and not within the processes. But anyway ;)

https://github.com/MarieLataretu/nextflow-mwe

[hoelzer]

@StefanFrankBio here another example of a small nf pipeline. I just worked on that one end of last year. For sure it's not perfect, but has the basic best practices in it:

https://github.com/hoelzer/pocp

And it hink it's easy to follow bc it's just a few modules (prokka, diamond, a custom script, ...)