Many thanksss to this fantastic session, in the past few days i’ve learned the HelloNextflow and Nextflow run courses, really clear instructions and easy to understand! i think i know the basic principles and logic in nextflow, but im still wonderding, if i want to write my own script and run it, what is the best way and best platform? (ie, is GitHub Codespace a good platform with proper java version, docker image utility and so on?)
Hi Rachel!
I would suggest having a local environment on your machine with Nextflow/Java installation as described here: Installation — Nextflow documentation
Then, for local scripts for your Nextflow pipelines, I would suggest following the nf-core pipeline standard way of doing it; putting your script in a bin/ folder, making it executable and then calling it through your Nextflow module. Example:
script: proteinfamilies/bin/filter_recruited.py at 4517bf0900a864da5ec0ab0eddfb23ccb57a0d14 · nf-core/proteinfamilies · GitHub
module: proteinfamilies/modules/local/filter_recruited/main.nf at 4517bf0900a864da5ec0ab0eddfb23ccb57a0d14 · nf-core/proteinfamilies · GitHub
Hope this helps!