elixir-no-nels / rbFlow-Germline

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

elixir-no-nels/rbFlow-Germline Issues

Time and file size optimizations
Updated 5 years ago5
Workaround i/o from/to shared filesystem
Closed 5 years ago1
Polish the start script
Closed 5 years ago1
Input folder flag (-i) limitation: /tsd/p172ncspm not supported
Closed 5 years ago2
Output folder flag (-o) limitation: /tsd/p172ncspm not supported
Closed 5 years ago2
TSV path flag (-t) limitation: the path /tsd/p172ncspm not supported
Closed 5 years ago2
Spark tools are officially recommended to not be used for production
Closed 5 years ago7
Exome capture kit bed file compatibility
Updated 6 years ago3
Put ruby in the container
Closed 6 years ago2
Update readme when the current milestone has been verified to work on TSD
Updated 6 years ago3
Define behavior and need for -p and -v options for rubyFlowLite cluster pipeline
Updated 6 years ago3
Blank slate setup and testing for the first release
Updated 6 years ago
Location of rubyFlowLite flag (-b) should be a configuration/installation item, not user exposed choice
Closed 6 years ago6
Reference location (-r) optimization
Closed 6 years ago7
Decide on choice of GATK version for the production release, 3.8, 4.0.2.0 or 4.0.8.1
Closed 6 years ago5
Support for multiple end user shared project disks
Updated 6 years ago1
Clearify if current Singularity version on Colossus is a showstopper for us
Closed 6 years ago2
Update help text to reflect more the output files than internals of the GATK pipeline when explaining options.
Closed 6 years ago3
We are missing a small test data, tsv and execution tests to validate the state of the code and implemented features
Closed 6 years ago1
Multi Sample support not keeping multiple samples in TSV input apart
Closed 6 years ago1
Interval file support fails
Closed 6 years ago1
Test issue
Closed 6 years ago1