Automated e2e test - Githubissues

VIB-PSB / MINI-AC

Motif-Informed Network Inference based on Accessible Chromatin (MINI-AC) is a method that combines accessible chromatin data from bulk or single-cell experiments with transcription factor binding site enrichment to learn gene regulatory networks in plants

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Automated e2e test #9

Closed hdbeukel closed 1 year ago

hdbeukel commented 1 year ago

Adds automated e2e tests for the main workflow. There are four test cases:

maize_v4 genome_wide
- with DE (1 gene set)
- network filtering (1 gene set)
- 2nd gene annotation
- no bps
maize_v4 locus_based
- no DE
- network filtering (1 gene set)
- with bps
arabidopsis genome_wide
- with DE (separate gene sets)
- no network filtering
- no 2nd gene annotation
- bps
arabidopsis locus_based
- no DE
- no network filtering
- no bps

hdbeukel commented 1 year ago

TODO before reviewing:

[ ] run on full example set (verify results manually)
[x] try to setup automated GitHub action to run tests for pushes and PRs to dev and main

hdbeukel commented 1 year ago

Wow @nicomaper thanks for the detailed review! I have skimmed through your comments and many make a lot of sense. I will fist answer your comments that are actually questions and then make some changes. I'll let you know when I am done.