Create an issue for each summary workflow that has to be implemented

[faricazjj]

I created issues for each broken down task based on @daneckaw 's list of things left to do for summary workflow:

1. General:
   1.1 Decide on what to do with optional plots/things to be visualized outside of OEB. See discussion here: utils: scripts for visualizing summary statistics outside OEB #245 - might be low priority, but it would be helpful for the paper: feat(Publication): Plot outside of OpenEBench #290
   1.2 Do we need to change any metrics based on results we already have?
2. Identification summary workflow :feat: identification summary workflow #239

• ongoing, see PR: feat: identification summary workflow #239
  2.1 Validation part of the workflow - needs to be revised, might be incomplete (e.g. see here Validation fails with mitochondrial genes #258): Identification summary workflow: test and update validation #300
  2.2 Functions for calculating simple metrics (precision, sensitivity) - ongoing (same PR), needs low level testing: feat: identification summary workflow #239
  2.3 Functions for calculating annotation-dependent metrics - not started, but similar examples already in quantification summary workflow: Identification summary workflow: implement annotation-dependent and other metrics #298
  2.4 Thorough high-level testing. Depends on completing tasks 2.1-2.3: Identification summary workflow: testing #297
  2.5 Optional metrics/plots (as in specification). Depends on completing tasks 1.1, 2.1-2.3
  2.6 Adjust identification ranking: Adjust identification ranking #308

3. Quantification summary workflow - workflow and metrics calculation functions done
   3.1 Additional testing/debugging ongoing: Quantification summary workflow: testing #299
   3.2 Optional metrics/plots (as in specification). Depends on completing task 1.1
4. Differential summary workflow: feat(Summary workflows): Differential summary workflow #294
   4.1 Workflow "backbone" - can be mostly copied from quantification, but input validation will be different: Differential summary workflow: backbone #292
   4.2 POC of metrics to be added: Differential summary workflow: metrics POC #293
   4.3 Implement Functions for calculating metrics (there is only one) - can be done independently of 4.1: Differential summary workflow: metrics implementation #295
   4.4 High level testing. Depends on completing tasks 4.1-4.2: Differential summary workflow: testing #296
   4.5 Adjust differential ranking: Adjust differential ranking #309

@daneckaw @dominikburri @mrgazzara let me know if there's anything I missed

[dominikburri]

Hi @faricazjj , thank you for the breakdown!
@txellferret and I are also working on the ranking parameter for the OEB plots (i.e. that the right corner is set to better) in PR #262. It is for the quantification swf, but should then be passed down to other swfs as well, for details see issue #242.

[faricazjj]

@dominikburri I see! Thank you for pointing it out, I'll add adjust identification ranking and adjust differential ranking to the list! :D

[faricazjj]

@dominikburri done! They're now under points 2.6 and 4.5

[faricazjj]

Closing this issue since all currently known summary workflow todos have issues created