elixir-no-nels/Selma

Issues

• Support for local execution

  #34 opened 5 years ago by oskarvid
  0

• Explore building the Singularity image with Travis

  #33 opened 5 years ago by oskarvid
  0

• Figure out how gvanno can fit in to the workflow

  #32 opened 5 years ago by oskarvid
  0

• Upgrade Singularity to the latest supported version on TSD

  #31 opened 5 years ago by oskarvid
  0

• Upgrade GATK to the latest version

  #30 opened 5 years ago by oskarvid
  0

• Potential issue if we officially support exome (interval file) data analysis

  #29 opened 5 years ago by oskarvid
  0

• Run hap.py on wgs output files

  #28 opened 5 years ago by oskarvid
  0

• Add version numbers where necessary

  #27 opened 5 years ago by oskarvid
  0

• Starting Selma

  #17 opened 5 years ago by daviddolan
  2

• Input folder requirements

  #22 opened 5 years ago by kjellp
  2

• Reconsider how the -e flag should function

  #25 opened 5 years ago by oskarvid
  0

• Inform user of which sample/s failed

  #26 opened 5 years ago by oskarvid
  0

• Move most or all command line options to the settings file

  #19 opened 5 years ago by oskarvid
  0

• Move current command line options to the settings file

  #23 opened 5 years ago by oskarvid
  1

• Remove code from the settings file

  #24 opened 5 years ago by oskarvid
  0

• Run one sample per node

  #5 opened 5 years ago by oskarvid
  4

• Required parameter "-o" not detected as missing if not present.

  #21 opened 5 years ago by kjellp
  2

• Enhance documentation of -s option

  #20 opened 5 years ago by kjellp
  1

• Put singularity image and master Selma copy in /tsd/shared/bioinformatics/

  #12 opened 5 years ago by oskarvid
  2

• Disk quota on Colossus is exceeded during execution

  #18 opened 5 years ago by oskarvid
  5

• Squeue is unstable on Colossus

  #16 opened 5 years ago by oskarvid
  1

• Clarify the purpose of the custom interval file support in the documentation

  #15 opened 5 years ago by oskarvid
  1

• Select specific sample from TSV file

  #3 opened 5 years ago by oskarvid
  3

• Squeue seems to be crashing the workflow

  #14 opened 5 years ago by oskarvid
  1

• TSD start-workflow.sh issues

  #13 opened 5 years ago by daviddolan
  3

• Figure out how to handle config options

  #11 opened 5 years ago by oskarvid
  1

• Documentation

  #10 opened 5 years ago by oskarvid
  1

• Snakemake config file - TSD

  #2 opened 6 years ago by oskarvid
  2

• Sbatch script failure handling

  #9 opened 6 years ago by oskarvid
  1

• Support for exome interval files

  #4 opened 6 years ago by oskarvid
  2

• File staging - TSD

  #8 opened 6 years ago by oskarvid
  3

• Support for b37 reference files - TSD

  #6 opened 6 years ago by oskarvid
  3

• TSV file - TSD

  #1 opened 6 years ago by oskarvid
  1

• Change Snakemake working directory for clean input and output file handling

  #7 opened 6 years ago by oskarvid
  1