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BenaroyaResearch
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bripipetools
tools for managing genomics pipelines at BRI
MIT License
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parse txt instead of html picard metrics
#124
spribitzer
closed
1 year ago
0
Clean up epigenetic tools
#123
spribitzer
opened
2 years ago
1
bripipetools issues overview
#122
spribitzer
opened
2 years ago
1
update docs for research db connection
#121
revengeofthepencil
closed
2 years ago
0
additional features for ATAC seq
#120
spribitzer
opened
3 years ago
0
Allow for pushing individual project MiXCR data to the Research Database
#119
Scott1009
opened
3 years ago
0
Generalize the tenxdb.py script
#118
Scott1009
opened
3 years ago
0
Allow for updating TCR project data.
#117
Scott1009
opened
3 years ago
0
Test for partial downloads from basespace
#116
Scott1009
opened
3 years ago
0
`bripipetools wrapup` trying to read `.DS_store`
#115
spribitzer
opened
3 years ago
0
Avoid double submissions with `bripipetools submit` to the batchfile
#114
spribitzer
opened
3 years ago
0
`fix_fastq.sh` errors with `.DS_store`
#113
spribitzer
opened
3 years ago
0
add stranded runtime option for workflows
#112
jaeddy
closed
7 years ago
1
Update option parsing
#111
jaeddy
closed
7 years ago
1
More docs updates
#110
jaeddy
closed
7 years ago
1
Update documentation
#109
jaeddy
closed
7 years ago
1
Add sample submit
#108
jaeddy
closed
7 years ago
1
Chipseq workflow parsing
#107
jaeddy
closed
7 years ago
1
Fix logging config
#106
jaeddy
closed
7 years ago
1
create new launch script in and use click to build command line interface
#105
jaeddy
closed
7 years ago
1
Add submit package
#104
jaeddy
closed
7 years ago
1
Reorg parsing methods
#103
jaeddy
closed
7 years ago
1
Add parsing modules for BRI and workflow-specific strings
#102
jaeddy
closed
7 years ago
0
Simplify test deps 3
#101
jaeddy
closed
7 years ago
1
Workflow io module
#100
jaeddy
closed
7 years ago
1
Simplify test deps round 2
#99
jaeddy
closed
7 years ago
1
Simplify test deps
#98
jaeddy
closed
7 years ago
0
Add db authentication
#97
jaeddy
closed
7 years ago
1
Tests currently unwieldy, hard to follow
#96
jaeddy
closed
7 years ago
0
Migrate sex verify
#95
jaeddy
closed
7 years ago
1
Specialized module/classes for BRI 'genomics' server
#94
jaeddy
opened
8 years ago
0
Move sex check verification out of `annotation` module
#93
jaeddy
closed
7 years ago
0
Streamline/refactor wrapper scripts
#92
jaeddy
opened
8 years ago
0
Add wrapup script
#91
jaeddy
closed
8 years ago
1
use environment configs to parametrize genlims database connection
#90
jaeddy
closed
8 years ago
1
Environment-specific config for db connection
#89
jaeddy
closed
8 years ago
0
break out classes for different types of annotators into separate submodules
#88
jaeddy
closed
8 years ago
1
Migrate globusgalaxy code
#87
jaeddy
closed
8 years ago
1
Global application wrapper script for flowcell operations
#86
jaeddy
closed
8 years ago
0
Migration of `globusgalaxy` module code
#85
jaeddy
closed
8 years ago
0
Workflow batch file IO
#84
jaeddy
opened
8 years ago
0
Annotation submodule organization
#83
jaeddy
closed
8 years ago
1
Refactor io tests
#82
jaeddy
closed
8 years ago
1
Debug sexcheck postprocess
#81
jaeddy
closed
8 years ago
1
Extend sexcheck output
#80
jaeddy
closed
8 years ago
1
add genlims ops method for querying for a field among sample ancestors
#79
jaeddy
closed
8 years ago
1
Summary output merging
#78
jaeddy
closed
8 years ago
1
Retrieving information from parent objects
#77
jaeddy
closed
8 years ago
0
Merging summary processing outputs
#76
jaeddy
closed
8 years ago
0
Db object timestamps
#75
jaeddy
closed
8 years ago
1
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