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m5imunovic
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curly-octo-train
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Add download URL to species_info for downloaded datasets
#117
m5imunovic
opened
8 months ago
0
Merge random and real sequences into single step
#116
m5imunovic
closed
8 months ago
1
Add initial pipeline thoughts
#115
m5imunovic
closed
8 months ago
1
Change output structure and remove digraph code
#114
m5imunovic
closed
8 months ago
1
Add CHM13 as an option for reference.py
#113
m5imunovic
closed
8 months ago
0
Remove digraph support
#112
m5imunovic
closed
7 months ago
0
Upgrade pre-commit hooks
#111
m5imunovic
closed
8 months ago
0
Feature/109 add test to pre commit
#110
m5imunovic
closed
8 months ago
0
Add tests to pre commit hooks
#109
m5imunovic
closed
8 months ago
0
Upgrade pre commit package versions
#108
m5imunovic
closed
8 months ago
0
Pre commit activation fixes
#107
m5imunovic
closed
8 months ago
2
Raw zip should be removed from dataset and used for the actual PT files
#106
m5imunovic
closed
8 months ago
0
Update the pipeline config
#105
m5imunovic
opened
8 months ago
0
Use hardlinks instead of symlinks
#104
m5imunovic
closed
8 months ago
0
Support hydra multirun threading
#103
m5imunovic
closed
7 months ago
1
Use hardlink instead of symlink for simulator profile
#102
m5imunovic
closed
8 months ago
0
Enable reads profile copying
#101
m5imunovic
closed
8 months ago
0
Allow to copy profile instead of creating symbolic link
#100
m5imunovic
closed
8 months ago
0
Enable regex filtering of the specific chromosome from reference
#99
m5imunovic
closed
8 months ago
0
Implement filtering by chromosome in sequencing simulation
#98
m5imunovic
closed
8 months ago
0
Introduce structured configs for independent scripts
#97
m5imunovic
closed
7 months ago
1
Start dataset pipeline guide document
#96
m5imunovic
closed
8 months ago
0
Move CMake to mamba dependencies
#95
m5imunovic
closed
8 months ago
0
Use hydra config for download CHM13 script
#94
m5imunovic
closed
8 months ago
0
Move cmake to mamba dependencies and update readme
#93
m5imunovic
closed
8 months ago
0
Set up pre-commit and add instructions
#92
m5imunovic
closed
8 months ago
0
Download CHM13 uses hydra config
#91
m5imunovic
closed
8 months ago
0
Add read sampling script
#90
m5imunovic
closed
9 months ago
0
Create a script for random sampling from FASTQ file using the specified percentage of reads
#89
m5imunovic
closed
9 months ago
0
Simplify how we use hydra config
#88
m5imunovic
closed
10 months ago
0
Update environment to newer versions
#87
m5imunovic
closed
11 months ago
0
Update read extraction scripts
#86
m5imunovic
closed
1 year ago
0
Save code state at article submission
#85
m5imunovic
closed
1 year ago
0
Save script utils
#84
m5imunovic
closed
1 year ago
0
Update config files
#83
m5imunovic
closed
1 year ago
0
Fix eval path problem and add description of missing changes to upstream
#82
m5imunovic
closed
1 year ago
0
Hydra has some problems with Path - use str instead
#81
m5imunovic
closed
1 year ago
0
Add new species configs
#80
m5imunovic
closed
1 year ago
0
Fix of-by-one error in file splitting
#79
m5imunovic
closed
1 year ago
0
Upgrade hydra package
#78
m5imunovic
closed
1 year ago
0
Adapt download script saving format for simulation tool.
#77
m5imunovic
closed
1 year ago
0
Use pre calculated rc map if exists
#76
m5imunovic
closed
1 year ago
0
Add helper script for downloading chm13 and spliting into chromosomes
#75
m5imunovic
closed
1 year ago
0
Feature/add pre commit
#74
m5imunovic
closed
1 year ago
0
Feature/adapt eval for post execution
#73
m5imunovic
closed
1 year ago
0
Fix objects that were not JSON serializable
#72
m5imunovic
closed
1 year ago
0
Postpone lja eval by storing necessary command inputs in file
#71
m5imunovic
closed
1 year ago
0
Fix part of the failing tests
#70
m5imunovic
closed
1 year ago
0
Export eval data for coverage based correction
#69
m5imunovic
closed
1 year ago
0
Speed up rc map calculation using mp pool
#68
m5imunovic
closed
1 year ago
0
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