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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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All-whitespace Contacts field crashes load_metadata
#124
ressy
opened
8 months ago
0
Chunked Box uploader should be made fault-tolerant like the older uploader is
#123
ressy
opened
1 year ago
0
Project name should implicitly fill as expected in experiment spreadsheets
#122
ressy
opened
1 year ago
0
Add new "mergereads" task for read-merging with PEAR
#121
ressy
closed
1 year ago
0
Refactor Box code and update auth-scraping URL
#120
ressy
closed
1 year ago
0
Need read merging task
#119
ressy
closed
1 year ago
0
Update Python req to >=3.8
#118
ressy
closed
1 year ago
0
Need a task for raw fastq.gz files
#117
ressy
closed
1 year ago
1
Box uploads should optionally set expiration on share links
#116
ressy
opened
3 years ago
1
Handle non-unicode characters in TaskMetadata
#115
ressy
closed
3 years ago
0
Handle non-unicode characters in TaskMetadata
#114
ressy
closed
3 years ago
0
Box auth setup should show access error for web server log
#113
ressy
opened
3 years ago
0
Version 0.0.5
#112
ressy
closed
3 years ago
0
Refactor unit tests and migrate to CircleCI
#111
ressy
closed
3 years ago
0
The tests are atrociously inefficient and disorganized
#110
ressy
closed
3 years ago
0
Migrate from Travis CI for automated testing
#109
ressy
closed
3 years ago
0
Call alignment completion callback only when run is complete
#108
ressy
closed
3 years ago
0
Invalid runs not actually skipped in IlluminaProcessor.refresh
#107
ressy
closed
3 years ago
2
Support for loading BCL stats files
#106
ressy
closed
4 years ago
0
Handle non-unicode CSV files
#105
ressy
closed
4 years ago
0
Add error property to Alignment class
#104
ressy
closed
4 years ago
0
Exceptions during alignment intake should trigger admin email
#103
ressy
opened
4 years ago
1
Non-unicode characters crash load_csv
#102
ressy
closed
4 years ago
1
Version 0.0.4
#101
ressy
closed
4 years ago
0
Fix contig labeling in task_assemble
#100
ressy
closed
4 years ago
0
Add tests for task classes
#99
ressy
closed
4 years ago
0
Contig assembly task mis-numbers contigs
#98
ressy
closed
4 years ago
0
Parse checkpoint.txt files correctly
#97
ressy
closed
4 years ago
0
Checkpoint.txt file in Alignment directories is not parsed correctly
#96
ressy
closed
4 years ago
0
Parse tasks as lowercase in experiment metadata.csv files
#95
ressy
closed
4 years ago
0
Parse sample file paths from disk
#94
ressy
closed
4 years ago
0
Inferring expected files from sample names is just awful
#93
ressy
closed
4 years ago
0
Task column in experiment metadata should be automatically lowercased
#92
ressy
closed
4 years ago
0
Failed alignments should be handled
#91
ressy
opened
4 years ago
2
Version 0.0.3
#90
ressy
closed
4 years ago
0
Ignore Box network log message at level INFO or below
#89
ressy
closed
4 years ago
0
File contents dumped to log for each Box upload
#88
ressy
closed
4 years ago
0
Add --version argument
#87
ressy
closed
4 years ago
0
Use Unix-style line endings in report CSV
#86
ressy
closed
4 years ago
0
Suppress duplicate log messages for skipped runs
#85
ressy
closed
4 years ago
0
Specify minimum versions for dependencies
#84
ressy
closed
4 years ago
0
Minimum versions for dependencies need to be specified
#83
ressy
closed
4 years ago
0
Run failure should be available via Run class and the report
#82
ressy
opened
4 years ago
0
Old runs skipped should only be logged once
#81
ressy
closed
4 years ago
0
Executable should support --version argument
#80
ressy
closed
4 years ago
0
Report should use Unix line endings
#79
ressy
closed
4 years ago
0
We need a task to just copy raw FASTQ to the processing directory
#78
ressy
opened
4 years ago
0
Release 0.0.2
#77
ressy
closed
4 years ago
0
Use flow cell ID in project work_dir names
#76
ressy
closed
4 years ago
0
Add flowcell property to Illumina run class
#75
ressy
closed
4 years ago
0
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