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NYU-Molecular-Pathology
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snsxt
bioinformatics pipeline framework for data analysis
GNU General Public License v3.0
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refactor AnalysisSampleTask into SampleTask
#46
stevekm
closed
6 years ago
0
Dev steve
#45
stevekm
closed
7 years ago
0
add sleep timer
#44
stevekm
closed
7 years ago
0
reduce logging level
#43
stevekm
closed
7 years ago
0
sns jobs being caught and Job objects generated before log file is created
#42
stevekm
closed
7 years ago
0
MuTect2_split printing tons of job IDs to email log
#41
stevekm
closed
7 years ago
0
logger filehandler paths getting printed repeatedly at end of analysis
#40
stevekm
closed
7 years ago
0
Dev steve
#39
stevekm
closed
7 years ago
0
Fix log level
#38
stevekm
closed
7 years ago
0
need to fork snsxt into more generic framework
#37
stevekm
opened
7 years ago
0
Fix loglevel
#36
varshini712
closed
7 years ago
0
refactor 'task_lists' into 'pipelines'
#35
stevekm
opened
7 years ago
0
SnsWESAnalysisOutput class not compatible with other sns pipeline outputs
#34
stevekm
opened
7 years ago
2
need small datasets for testing
#33
stevekm
opened
7 years ago
0
need mini targets & probes for testing
#32
stevekm
closed
7 years ago
1
mutt does not work on cluster nodes
#31
stevekm
closed
7 years ago
2
refactor sns_task submodule names
#30
stevekm
opened
7 years ago
0
refactor analysis report to utilize sns analysis steps
#29
stevekm
opened
7 years ago
1
MuTect2 split jobs task
#28
stevekm
closed
7 years ago
1
Move binary configs to parent directory
#27
stevekm
opened
7 years ago
0
Move log dir to parent directory
#26
stevekm
opened
7 years ago
2
Separate log file for each analysis, sample, and task
#25
stevekm
opened
7 years ago
0
Integrate QC checks in reports and program output
#24
stevekm
opened
7 years ago
0
added sns start email
#23
varshini712
closed
7 years ago
1
Email not going to inbox
#22
varshini712
closed
7 years ago
2
Need running tasks to kill their jobs on error
#21
stevekm
opened
7 years ago
4
Need backup email notification in case of email send failure
#20
stevekm
opened
7 years ago
0
Need program framework dependency graph
#19
stevekm
closed
7 years ago
1
need to kill all qsub jobs if the program breaks
#18
stevekm
closed
7 years ago
0
need to adjust log message levels
#17
stevekm
opened
7 years ago
2
send email when analysis starts
#16
stevekm
closed
7 years ago
3
Skip analysis task if output already exists
#15
stevekm
opened
7 years ago
1
test update
#14
stevekm
closed
7 years ago
0
Travis CI not reporting failed tests
#13
stevekm
opened
7 years ago
1
Tasks might not be executed in order
#12
stevekm
closed
7 years ago
0
Can't run the same analysis task multiple times
#11
stevekm
closed
7 years ago
1
Need pipeline tasks for sns pipeline routes
#10
stevekm
closed
7 years ago
0
Revise analysis sample output file path retrieval
#9
stevekm
closed
7 years ago
3
Need to have background qsub job queue for the program
#8
stevekm
closed
7 years ago
2
Need more error checking of analysis task output
#7
stevekm
closed
7 years ago
0
Create LICENSE
#6
stevekm
closed
7 years ago
0
Include CNV analysis
#5
stevekm
opened
7 years ago
0
include mail output
#4
stevekm
closed
7 years ago
0
Return error code or process object from subprocess functions
#3
stevekm
opened
7 years ago
0
annotate-peaks submodule breaks Travis build
#2
stevekm
closed
7 years ago
1
integrate sns pipeline with snsxt
#1
stevekm
closed
7 years ago
1