How do imports work with python scripts that live in

/template

. I have a process that runs a python script like this:

script:
    template("script1.py")

script1.py

imports

script2.py

which lives inside the

template/

folder. Running the module produces an error about missing imports "ModuleNotFoundError"

Nextflow writes the template file to the workDir, so

script1.py

is created as a new file in the

workDir

with the variables interpreted. This means your import script doesn't exist unless you also stage it and make it available in the

PYTHONPATH

somehow.

That seems not correct - the template use here causes the

script

session to get the value of the evaluated template - but that ends up in

.command.sh

. It may be a better design to go with binaries rather than templates.

That seems not correct - the template use here causes the

script

session to get the value of the evaluated template - but that ends up in

.command.sh

.

Yes, sorry that's what I was trying (and failing) to say

Dang, I was hoping to keep the python files separate.