Add a best practice page describe how to run Python scripts

[pditommaso]

The goal of this issue is to improve the documentation by adding a best practice section dedicated to the user of Python code and script with Nextflow

[bentsherman]

@christopher-hakkaart adding to your docket as I won't be able to start it anytime soon. Not urgent but nice to have. @vdauwera might be able to help once you have a first draft.

This page should basically expand on this sentence we added recently about template scripts:

The best practice for using a custom script is to embed it in the process definition at first and move it to a separate file with its own command line interface once the code matures.

I imagined it as a tutorial that focuses on Python scripts. We would write a small pipeline that wires together 2-3 python scripts:

1. Start with each script embedded in the process definition
2. In a second iteration, move each script into a separate file, add a CLI to it using argparse, and call the script like a regular command-line tool from the process definition

The main thing we want to show is the design of the CLI for each Python script based on the process inputs/outputs. This is the best practice for custom Python scripts with Nextflow but we don't have any material on it.

The main question is what should the pipeline be. My hyperopt pipeline might be too complex, so maybe we could do some simple text processing instead. You could take the your first script example or something from the training and replace the bash commands with Python scripts.

[christopher-hakkaart]

Nice idea. I think we should keep this simple to isolate the learning objectives. Maybe this could be a spin-off from the hello series @vdauwera + others are developing. However, it might be easier to have an independent "Convert your Python script using best practices" guide.

Either way, requiring domain knowledge might work against us, so simple scripts that perform simple operations might be best. I'll think about it and come up with a proposal.

[bentsherman]

If it would fit well in the training material, I'm fine with that as well

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.