hi does someone know if there is a

zarr

structure in the

test-dataset

repo?

not as far as I know. But public s3 should also work I assume?

I assume you need the data for

tests

? I think we've just found out that using a bespoke url to some random bucket does work with

nf-test

but not

nf-core modules test

. Since the later one overwrites

params.modules_testdata_base_path

So, better to PR one minimal test data to

test-datasets

i will have a look but what i also noticed is that github raw cannot be used for a directory? maybe i also using it wrong somehow but for zarr it didn’t work for me. And yes i need it as a test dataset. For now my pragmatic workaround for the module

raw2ometiff

was to include a zarr image so i can have the relative path for my tests.

actually, according to @Kobe Lavaerts if you add the last line here:

name "Test Process IMAGESEGMENTATIONMETRICS"
    script "../main.nf"
    process "IMAGESEGMENTATIONMETRICS"
    config "./nextflow.config"

it should take your nextflow.config file in the

tests

folder

A ZipStorage zarr should work with a github raw URL (rather than a DirectoryStorage zarr). For a tiny test example it shouldn't be a problem to have all the chunks in one zip file.

I assume one will need to unzip for accessing? Or use a zipstore specific loader?

Depends on which library is being used to access it. The Python

zarr.open

function for example should just automatically do the right thing.

I guess we need to give it a try 🙂 ? - Didn't know that

zarr.open

can do that! Will give it a try!

(It’s being readded for zarr v3 😉)