NYU-Molecular-Pathology/snsxt

Issues

• need to fork snsxt into more generic framework

  #37 opened 7 years ago by stevekm
  0

• logger filehandler paths getting printed repeatedly at end of analysis

  #40 opened 7 years ago by stevekm
  0

• sns jobs being caught and Job objects generated before log file is created

  #42 opened 7 years ago by stevekm
  0

• MuTect2_split printing tons of job IDs to email log

  #41 opened 7 years ago by stevekm
  0

• Move log dir to parent directory

  #26 opened 7 years ago by stevekm
  2

• need to adjust log message levels

  #17 opened 7 years ago by stevekm
  2

• SnsWESAnalysisOutput class not compatible with other sns pipeline outputs

  #34 opened 7 years ago by stevekm
  2

• refactor 'task_lists' into 'pipelines'

  #35 opened 7 years ago by stevekm
  0

• need mini targets & probes for testing

  #32 opened 7 years ago by stevekm
  1

• need small datasets for testing

  #33 opened 7 years ago by stevekm
  0

• refactor sns_task submodule names

  #30 opened 7 years ago by stevekm
  0

• Include CNV analysis

  #5 opened 7 years ago by stevekm
  0

• Travis CI not reporting failed tests

  #13 opened 7 years ago by stevekm
  1

• Need running tasks to kill their jobs on error

  #21 opened 7 years ago by stevekm
  4

• refactor analysis report to utilize sns analysis steps

  #29 opened 7 years ago by stevekm
  1

• Need backup email notification in case of email send failure

  #20 opened 7 years ago by stevekm
  0

• Integrate QC checks in reports and program output

  #24 opened 7 years ago by stevekm
  0

• Separate log file for each analysis, sample, and task

  #25 opened 7 years ago by stevekm
  0

• mutt does not work on cluster nodes

  #31 opened 7 years ago by stevekm
  2

• Email not going to inbox

  #22 opened 7 years ago by varshini712
  2

• Skip analysis task if output already exists

  #15 opened 7 years ago by stevekm
  1

• send email when analysis starts

  #16 opened 7 years ago by stevekm
  3

• Can't run the same analysis task multiple times

  #11 opened 7 years ago by stevekm
  1

• MuTect2 split jobs task

  #28 opened 7 years ago by stevekm
  1

• Move binary configs to parent directory

  #27 opened 7 years ago by stevekm
  0

• Need program framework dependency graph

  #19 opened 7 years ago by stevekm
  1

• need to kill all qsub jobs if the program breaks

  #18 opened 7 years ago by stevekm
  0

• Need more error checking of analysis task output

  #7 opened 7 years ago by stevekm
  0

• Need pipeline tasks for sns pipeline routes

  #10 opened 7 years ago by stevekm
  0

• include mail output

  #4 opened 7 years ago by stevekm
  0

• Tasks might not be executed in order

  #12 opened 7 years ago by stevekm
  0

• Revise analysis sample output file path retrieval

  #9 opened 7 years ago by stevekm
  3

• Need to have background qsub job queue for the program

  #8 opened 7 years ago by stevekm
  2

• integrate sns pipeline with snsxt

  #1 opened 7 years ago by stevekm
  1

• Return error code or process object from subprocess functions

  #3 opened 7 years ago by stevekm
  0

• annotate-peaks submodule breaks Travis build

  #2 opened 7 years ago by stevekm
  1