elixir-no-nels/rbFlow-Germline

Issues

• Time and file size optimizations

  #16 opened 6 years ago by oskarvid
  5

• Workaround i/o from/to shared filesystem

  #21 opened 5 years ago by kjellp
  1

• Polish the start script

  #18 opened 6 years ago by oskarvid
  1

• Input folder flag (-i) limitation: /tsd/p172ncspm not supported

  #5 opened 6 years ago by oskarvid
  2

• Output folder flag (-o) limitation: /tsd/p172ncspm not supported

  #6 opened 6 years ago by oskarvid
  2

• TSV path flag (-t) limitation: the path /tsd/p172ncspm not supported

  #7 opened 6 years ago by oskarvid
  2

• Spark tools are officially recommended to not be used for production

  #22 opened 6 years ago by oskarvid
  7

• Exome capture kit bed file compatibility

  #20 opened 6 years ago by oskarvid
  3

• Put ruby in the container

  #17 opened 6 years ago by oskarvid
  2

• Update readme when the current milestone has been verified to work on TSD

  #14 opened 6 years ago by oskarvid
  3

• Define behavior and need for -p and -v options for rubyFlowLite cluster pipeline

  #2 opened 6 years ago by oskarvid
  3

• Blank slate setup and testing for the first release

  #19 opened 6 years ago by oskarvid
  0

• Location of rubyFlowLite flag (-b) should be a configuration/installation item, not user exposed choice

  #8 opened 6 years ago by oskarvid
  6

• Reference location (-r) optimization

  #9 opened 6 years ago by oskarvid
  7

• Decide on choice of GATK version for the production release, 3.8, 4.0.2.0 or 4.0.8.1

  #11 opened 6 years ago by oskarvid
  5

• Support for multiple end user shared project disks

  #13 opened 6 years ago by kjellp
  1

• Clearify if current Singularity version on Colossus is a showstopper for us

  #15 opened 6 years ago by kjellp
  2

• Update help text to reflect more the output files than internals of the GATK pipeline when explaining options.

  #10 opened 6 years ago by oskarvid
  3

• We are missing a small test data, tsv and execution tests to validate the state of the code and implemented features

  #12 opened 6 years ago by oskarvid
  1

• Multi Sample support not keeping multiple samples in TSV input apart

  #4 opened 6 years ago by oskarvid
  1

• Interval file support fails

  #3 opened 6 years ago by oskarvid
  1

• Test issue

  #1 opened 6 years ago by oskarvid
  1