NGS_Automated-2.0.15

• processGsRawData.sh:
  • Improved sanity check.
  • Allow multiple lanes per sample potentially from multiple flowcells.
  • Removed blank lines.
  • Updated for changed commandline args in createInhouseSamplesheetFromGS.py.
  • Changed format of control file created when the script is finished to make it in sync with the one demultiplexing.sh creates and which copyRawDataToPrm.sh expects.
• createInhouseSamplesheetFromGS.py major rewrite:
  • Improved sanity check.
  • Allow mutiple lanes per sample potentially from multiple flowcells
  • Standardized variable naming consistent with other scripts from this same repo
  • Simplified nested data structures by removing unused levels of nesting.
  • Use standard Python logging facility as opposed to writing a custom log file.
• copyRawDataToPrm.sh:
  • Removed non-working email commandline option
  • Added commandline option to specify an alternative SCR_ROOT_DIR to use as root on the source server.
• boxy.umcg-gd-dm.cron: Updated for new version numbers and option to specify an alternative SCR_ROOT_DIR to use as root on the source server for copyRawDataToPrm.sh.