If i was to curate a minimal dataset for testing of the CellProfiler modules, where would it go inside the repository? And if I were to add a README with download instructions for a larger test dataset, where would it go?

https://nf-co.re/docs/tutorials/tests_and_test_data/test_data#pipelines And bigger test data should be uploaded to s3 via a core member https://nf-co.re/docs/checklists/community_governance/core_team#uploading-test-data-to-s3-bucket

you do have a cellpainting branch in https://github.com/nf-core/test-datasets/tree/cellpainting

Just chiming in here as well, that Nextflow handles staging s3 paths seemlessly. So ideally, we'd have two "samplesheets" for test data present in the test-datasets branch with the only difference is that one of them points to

<https://raw.githubusercontent.com/>

paths and the other points to

<s3://cellpainting-gallery>

paths. You can see an example of that here for rnaseq in the

samplesheet_test.csv

and

samplesheet_full.csv

. https://github.com/nf-core/test-datasets/tree/rnaseq/samplesheet