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WayScience
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CytoSnake
Orchestrating high-dimensional cell morphology data processing pipelines
https://cytosnake.readthedocs.io
Creative Commons Attribution 4.0 International
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Implementing CytoSnake testing frame work
#49
axiomcura
opened
1 year ago
0
Implement PyTest fixtures for teardown code
#48
axiomcura
opened
1 year ago
0
Replace `os` library with `pathlib` in workflow scripts
#47
axiomcura
closed
1 year ago
1
Add barcode logic to CytoSnake's CLI
#46
axiomcura
closed
1 year ago
2
Allow CytoSnake to default to `mamba` as default package manager
#45
axiomcura
closed
1 year ago
2
Improving Pathing system
#44
axiomcura
closed
1 year ago
0
Add `CytoTable` module to have `csv` and `npz` support
#43
axiomcura
opened
1 year ago
0
Allow multiple metadata directories for a single CytoSnake run
#42
axiomcura
opened
1 year ago
0
Reduce complexity in `CytoSnake` scripts
#41
axiomcura
opened
1 year ago
1
Reduce complexity in `get_config_fpaths()` when generating `_paths.yaml` meta config
#40
axiomcura
opened
1 year ago
0
Update ReadME
#39
axiomcura
closed
1 year ago
0
Make General Config Name more Specific
#38
axiomcura
opened
1 year ago
0
New Workflow: `cp_process_singlecells` !
#37
axiomcura
closed
1 year ago
7
Add auto complete support to CLI
#36
axiomcura
opened
1 year ago
0
`get_project_dir()` is buggy :lady_beetle:
#35
axiomcura
opened
1 year ago
1
Make `mamba` as Snakeamke's default environment manager
#34
axiomcura
closed
1 year ago
1
Decoupling rule modules into individual components
#33
axiomcura
closed
1 year ago
1
Make helper functions more generalizable
#32
axiomcura
closed
1 year ago
0
Helper function implementation
#31
axiomcura
closed
1 year ago
1
Pre commit formatting applied
#30
axiomcura
closed
1 year ago
0
Repeated code block pattern
#29
axiomcura
closed
1 year ago
0
Circular import error when moving `transport_project_files()` to `file_utils` module
#28
axiomcura
opened
1 year ago
0
Rename `fpaths` to `file_paths` for consistency and improved readability
#27
axiomcura
opened
1 year ago
0
CytoSnake New Pathing implementation
#26
axiomcura
closed
1 year ago
4
Adding pre-commit documentation
#25
axiomcura
closed
1 year ago
0
adding pre-commit hooks
#24
axiomcura
closed
1 year ago
5
Create a script that bundles all the required files for `CytoSnake` tutorial
#23
axiomcura
opened
1 year ago
0
Related work
#22
shntnu
opened
1 year ago
0
Platemap Index Error Not Called
#21
jenna-tomkinson
opened
1 year ago
1
CytoSnake Sphinx Documentation
#20
axiomcura
closed
1 year ago
1
Renaming `CytoPipe` to `CytoSnake`
#19
axiomcura
closed
2 years ago
0
Unable to import `cytosnake` helper functions causes repetitive code within workflow scripts
#18
axiomcura
opened
2 years ago
1
Implementing `dp_process` into `cytosnake`
#17
axiomcura
closed
2 years ago
2
CLI argument handler restructuring
#16
axiomcura
closed
2 years ago
1
CytoPipe CLI implementation
#15
axiomcura
closed
2 years ago
2
Logging implementation for CytoPipe
#14
axiomcura
closed
2 years ago
1
Creating intuitive .smk file name(s)
#13
gwaybio
opened
2 years ago
0
Config file and default parameters required for `consensus.py` script
#12
axiomcura
closed
2 years ago
1
Removed Multi-processing and replaced it with `Snakemake's` native multiprocessing support
#11
axiomcura
closed
2 years ago
5
Multi-processing implementation in aggregation
#10
axiomcura
closed
2 years ago
0
Improve Logging system
#9
axiomcura
opened
2 years ago
1
Implementing iterative support for CytoPipe
#8
axiomcura
closed
2 years ago
0
Implementing iterative support for CytoPipe
#7
axiomcura
closed
2 years ago
0
Feature Select Implementation to CytoPipe
#6
axiomcura
closed
2 years ago
0
Config file implementation and added `snakefmt` and `dry run` tests documentation
#5
axiomcura
closed
2 years ago
1
Add details to implement dry run and formatting style in README
#4
gwaybio
closed
2 years ago
1
Initial DAG implementation
#1
axiomcura
closed
2 years ago
5
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