I'm looking to fix an include of a non standard ext key in cellranger multi https://github.com/nf-core/modules/blob/master/modules/nf-core/cellranger/multi/main.nf and I just noticed the python template is just there to write out a config file.

cellranger

is run through the script as a normal cli call. I feel like this module would be better implemented using pure groovy and bash, rather than a mix of groovy, python, and bash. What are your takes on this?

Well, looking at it, it seems to be quite a complicated python script though, with the generation of a config file and conditional bits

Oh, wow. That's even simpler. That should definitely not be a pattern we should be supporting in my opinion. It just obfuscates code.

I think that cellranger multi may be complicated enough to support the python script, it certainly isn't immediately obvious to me what it is doing and how to put that into bash. But definitely the new PR is just some bash script

My pattern would be to construct the map in groovy, and use a TOML writer. Same pattern as QUARTONOTEBOOK.

yeah, which is complicated and hard to understand too 🤷