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ShawHahnLab
/
umbra
Python package and executable for Linux for managing Illumina sequencing runs
GNU Affero General Public License v3.0
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Catch all metadata.csv exceptions when setting up projects
#74
ressy
closed
4 years ago
0
Better metadata parsing
#73
ressy
closed
4 years ago
0
ProjectData work_dir can collide for simultaneous runs under same project
#72
ressy
closed
4 years ago
1
Blank rows should be ignored in metadata spreadsheet
#71
ressy
closed
4 years ago
0
Systemd service should support reload command
#70
ressy
opened
4 years ago
0
Add chunked approach to box uploader
#69
ressy
closed
4 years ago
0
Box uploads should be using chunked approach
#68
ressy
closed
4 years ago
0
Directory timestamp not reliable for min_age feature
#67
ressy
closed
4 years ago
1
Timeout feature for manual and geneious tasks
#66
ressy
closed
4 years ago
0
Invalid metadata spreadsheet should be handled
#65
ressy
closed
4 years ago
1
Remove quote characters when matching sample names to file names
#64
ressy
closed
5 years ago
0
Make ProjectData sample_paths setter handle None
#63
ressy
closed
5 years ago
0
sample paths properties should exclude quote characters
#62
ressy
closed
5 years ago
0
Missing FASTQ case in project setup crashes procecessor
#61
ressy
closed
5 years ago
0
Manual processing should allow timeout
#60
ressy
closed
4 years ago
0
Handle missing experiment entry in sample sheets
#59
ressy
closed
5 years ago
0
Runs with unspecified experiment should be handled during processing
#58
ressy
closed
5 years ago
0
Reorganize Box uploader tests and extend
#57
ressy
closed
5 years ago
0
Support for custom Task classes
#56
ressy
closed
5 years ago
0
Version 0.0.1
#55
ressy
closed
5 years ago
0
Store version string in package
#54
ressy
closed
5 years ago
0
Refactor package
#53
ressy
closed
5 years ago
0
Add retry feature for Box uploads
#52
ressy
closed
5 years ago
0
BoxUploader should have retry feature for upload failure
#51
ressy
closed
5 years ago
0
Duplicate sample name case should be handled
#50
ressy
opened
5 years ago
1
Email task reorganization
#49
ressy
closed
5 years ago
0
Add integration tests and fix null task list handling
#48
ressy
closed
5 years ago
0
Test tasks
#47
ressy
closed
5 years ago
0
Tidy code structure in umbra and test_umbra packages
#46
ressy
closed
5 years ago
0
Custom tasks should be supported via configuration file
#45
ressy
closed
5 years ago
0
Metadata output not respecting configured output path for implicit tasks
#44
ressy
closed
5 years ago
1
Always explicit tasks
#43
ressy
closed
5 years ago
0
Move contig assembly into "spades" task
#42
ressy
closed
5 years ago
0
Modularize tasks into separate classes
#41
ressy
closed
5 years ago
0
Email notices should include run and experiment identifiers
#40
ressy
closed
5 years ago
0
Fix directory path bug in copy_metadata
#39
ressy
closed
5 years ago
0
Allow bare email addresses in experiment metadata
#38
ressy
closed
5 years ago
0
Metadata parsing should accept bare email addresses
#37
ressy
closed
5 years ago
0
Keep Geneious dependency outputs at top level
#36
ressy
closed
5 years ago
0
Add lab-specific task "geneious"
#35
ressy
closed
5 years ago
0
Support configurable parent directories for task outputs
#34
ressy
closed
5 years ago
0
Optionally store implicit task dependency output in configurable subdirectory
#33
ressy
closed
5 years ago
1
Store task logs under configurable subdirectory
#32
ressy
closed
5 years ago
1
Fix relative import of illumina.run.Run
#31
ressy
closed
5 years ago
0
General cleanup with pylint
#30
ressy
closed
5 years ago
0
Handle sample name mismatches between metadata.csv and SampleSheet.csv
#29
ressy
closed
5 years ago
0
Handle sample name mismatches between metadata.csv and SampleSheet.csv
#28
ressy
closed
5 years ago
0
Handle byte order mark in CSV files
#27
ressy
closed
5 years ago
0
load_sample_sheet fails if unicode byte order mark is included
#26
ressy
closed
5 years ago
1
Don't overwrite a custom config with default during install
#25
ressy
closed
5 years ago
0
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