bioinfonerd / CyCif_Manager

Manage CyCIF Pipeline on HMS O2

bioinfonerd/CyCif_Manager Issues

Add CODEX flexibility to pipeline
Updated 5 years ago
Allow pipeline to be started at any point
Updated 5 years ago
Change example data permissions
Updated 5 years ago
Parallelize Pipeline
Updated 5 years ago
Testing environment Ignore Transfer
Updated 5 years ago1
Remove Old Environments from History
Closed 5 years ago1
Expose sbatch requirements
Updated 5 years ago
Update documentation
Closed 5 years ago1
Data stored on Imstor isn't exposed to python program
Updated 5 years ago1
Python programs aren't callable by command line
Closed 5 years ago1
Add more comments for each component of pipeline
Updated 5 years ago
Illumination Program: Field Correction as possible yaml parameter
Closed 5 years ago1
Add TMA Functionality
Updated 5 years ago
ashlar parameter add
Updated 5 years ago1
Add version tracking for module and environments
Updated 5 years ago
Add basic testing
Updated 5 years ago
change unet libraries to local environment
Closed 5 years ago1
setup O2 pipeline developer test space
Updated 5 years ago
What nucleus channel should be used for segmentation?
Updated 5 years ago
fix ashlar not running if already ran
Updated 5 years ago
add summation of time takes to run pipeline
Updated 5 years ago
HMS-RC suggests using transfer server instead of transfer partition
Closed 5 years ago1
Segmentation not handling multiple files correctly
Updated 5 years ago
Feature extraction not being organized correctly
Updated 5 years ago
Upload to Omero automatically
Updated 5 years ago
Add ability for developer submodules
Updated 5 years ago
Checkpoints to stop the pipeline if one of the modules does not produce an output
Updated 5 years ago
add job id to a pipeline run otherwise error/output logs will overwrite
Updated 5 years ago