elixir-no-nels rbFlow-Germline issues

elixir-no-nels / rbFlow-Germline

A workflow engine with a germline calling pipeline running in a container

MIT License

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Spark tools are officially recommended to not be used for production

#22 oskarvid closed 5 years ago
7
Workaround i/o from/to shared filesystem

#21 kjellp closed 5 years ago
1
Exome capture kit bed file compatibility

#20 oskarvid opened 5 years ago
3
Blank slate setup and testing for the first release

#19 oskarvid opened 5 years ago
0
Polish the start script

#18 oskarvid closed 5 years ago
1
Put ruby in the container

#17 oskarvid closed 5 years ago
2
Time and file size optimizations

#16 oskarvid opened 6 years ago
5
Clearify if current Singularity version on Colossus is a showstopper for us

#15 kjellp closed 6 years ago
2
Update readme when the current milestone has been verified to work on TSD

#14 oskarvid opened 6 years ago
3
Support for multiple end user shared project disks

#13 kjellp opened 6 years ago
1
We are missing a small test data, tsv and execution tests to validate the state of the code and implemented features

#12 oskarvid closed 6 years ago
1
Decide on choice of GATK version for the production release, 3.8, 4.0.2.0 or 4.0.8.1

#11 oskarvid closed 6 years ago
5
Update help text to reflect more the output files than internals of the GATK pipeline when explaining options.

#10 oskarvid closed 6 years ago
3
Reference location (-r) optimization

#9 oskarvid closed 6 years ago
7
Location of rubyFlowLite flag (-b) should be a configuration/installation item, not user exposed choice

#8 oskarvid closed 6 years ago
6
TSV path flag (-t) limitation: the path /tsd/p172ncspm not supported

#7 oskarvid closed 5 years ago
2
Output folder flag (-o) limitation: /tsd/p172ncspm not supported

#6 oskarvid closed 5 years ago
2
Input folder flag (-i) limitation: /tsd/p172ncspm not supported

#5 oskarvid closed 5 years ago
2
Multi Sample support not keeping multiple samples in TSV input apart

#4 oskarvid closed 6 years ago
1
Interval file support fails

#3 oskarvid closed 6 years ago
1
Define behavior and need for -p and -v options for rubyFlowLite cluster pipeline

#2 oskarvid opened 6 years ago
3
Test issue

#1 oskarvid closed 6 years ago
1