Set up test profile - Githubissues

nf-core / mcmicro

An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

https://nf-co.re/mcmicro

MIT License

4 stars 12 forks source link

Set up test profile #20

Closed jmuhlich closed 3 months ago

jmuhlich commented 3 months ago

Description of feature

The test profile should run our small tonsil test image data through as much of the pipeline as we have working.

RobJY commented 3 months ago

From the rnaseq repo it looks like we should have the input parameters in the test-dataset repo so we can use URLs in test.config and related files. Is this correct or should I just try to use the files from our assets directory?

Should we do multiple test profiles like:

test: minimal run using 1 row per sample per cycle samplesheet with no illumination correction so we just need input_cycle and marker_sheet parameters.
test_cycle_basicpy: same as test, but include basicpy illumination correction
test_sample_basicpy: minimal run using 1 row per sample samplesheet with basicpy illumination correction

RobJY commented 3 months ago

We may want to improve the quality of the sample and marker sheets before we put them in the test data repo since I just put in garbage values to have something to run.

RobJY commented 3 months ago

I'm already using URLs for the 1 row per sample per cycle samplesheets, but I still have full paths in the ones for 1 row per sample because they require an image_directory. I guess we could specify an S3 bucket 'directory'? Is there a better way to do this?

jmuhlich commented 3 months ago

I hacked something together in the recent PR that was just merged to dev. It uses a local sample sheet that's committed to the mcmicro repo, but I reference it via its raw.githubusercontent.com URL. I think the correct long-term solution is to commit the test samplesheets and marker sheets to the (as yet nonexistent) mcmicro branch in the test-datasets repo and reference them by https URL from there.

jmuhlich commented 3 months ago

Since #26 also introduces a minimally functional test profile and our CI now requires it to run successfully, I'll close this. We can improve the test profile setup with a more expansive sample sheet as time goes on.