Philosophical question: there is an nf-core module (picard/fastqtosam) that doesn't do exactly what I need -- it doesn't name the output filename with the convention I need. The module doesn't provide much functionality so I could just write my own process. What is best practice in this situation?

You can update the module and open a PR or use

nf-core modules patch

to make changes in your local repo :)

depending on what you need, you could just edit

ext.prefix

through a config file

Ah, ok, that's what I need to learn how to do

Sure, you can use closures based on values in your

meta

map

problem with editing the map is that I want SAMPLE_NAME and output filename to be different

Shouldn’t be an issue 🤷🏻