Sage-Bionetworks-Challenges / Multi-seq-Data-Analysis-DREAM-Challenge-Infra

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Update Tested Workflow for Live - dataset1 of SC1 #1

Closed rrchai closed 2 years ago

rrchai commented 2 years ago

TO-DO List:

[x] change admin to organizer team
[x] find optimal docker memory limit
[x] enable to modify prop and condition in workflow
[x] enable to load gs for different quesionts
[x] enable to run subchallenge-specific workflow

scRNAseq:

Validation:

[x] have all required files
[x] row and column names matched
[x] values are numeric
[x] value are => 0
[x] if current format of filenames is safe to be potentially shown in the validation or log file

Scoring:

[x] primary (chdir)
[x] secondary (nrsme)
[x] upload scoring script

scATACseq:

TBD - wait for reference scripts

Hold:

[ ] aggregate scores and display result by test case # may not need until post-analysis
[ ] scripts to breaking tie # may need to run bootstrap on predictions, but it will increase running time
[ ] instead of downloading gs from synapse, read via docker locally # it can speed up a bit, but optional for now

vpchung commented 2 years ago

Good start, @rrchai ! 🚀