dear microscopy people, I've made a nf-core compatible

subworkflow

which uses several modules for tiled segmentation. which can be found here: https://github.com/BioinfoTongLI/modules/blob/develop/subworkflows/sanger/tiled_segmentation/main.nf I wonder what is best practice to built the subworkflow from

nextflow

perspective. Is it better to

include all modules into one subworkflow

as it currently is OR construct

one subworkflow per method

? i.e. 4 subworkflows in total in my case? PS:Please ignore the module names etc. I will push them to the main stream soon to make sure all is in

nf-core

Hey @Tong LI , That's a really good question. I think both are valid approaches but personally I prefer the one that you have in your repo right now. The approach of having these different segmentation methods within that one subworkflow group them thematically in the "tiled segmentation" way of segmentation. Putting each in their own subworkflow in my opinion would just create more complexity that is easily solved via

if ... else

statements in your subworkflow.

Hi @Florian Wuennemann, thanks for the comments! I will try to push this version to the main stream then. I've actually got another questions regarding test data. For the segmentation modules, they are using the one in

test-datasets

repo. But for merging the polygons. I don't think there are any

wkt

or

geojson

files yet. Am I right?

If they aren't in this folder, i highly doubt these file types exist yet in test-datasets. Feel free to make a PR to add them! https://github.com/nf-core/test-datasets/tree/modules/data/imaging

also a small technical detail. I heard that nextlfow now support

switch ... case

. is that preferred compared to

if ... else

?

The strict syntax doesn't support switch/case, so you should use if/else for now. I might try to add pattern matching later on

I'd recommend checking out the latest podcast, this is one of the things we discussed 🙂 (can find it in the transcript if you like)

thanks!