NGS_Automated-3.0.2

Merge pull request #166 from RoanKanninga/master

added searching in all prm when searching for ConcordanceCheck ngs vcfs

NGS_Automated-3.0.1

new

• timing script that can be imported into molgenis

ConcordanceCheck:

• added ConcordanceCheck from GAP repo to NGS_Automated
• made new script that makes a samplesheet

changed

NGS_Automated-2.0.18

• bugfix: declaring array IFS problem
• improved logging
• added timing script for every step in the pipeline
  • demultiplexingTiming (1 hour)
  • copyRawDataToPrmTiming (6 hours)
  • pipelineTiming
    • generateScripts (5 hours)
    • startPipeline (6 hours)
    • copyProjectDataToPrm (6 hours)

NGS_Automated-2.0.17

bugfix: removing the moving of the .failed file twice

NGS_Automated-2.0.16

• Proper handling of situation when there are no samplesheets to process.

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.

NGS_Automated-2.0.14

bugfix in copyRawDataToPrm, when mv can be done, don't do the move again

NGS_Automated-2.0.13

• fix when counting files on chaperone (chaperone thinks that symlinks are files too)
  -added moving of the samplesheet on gattaca/zf.ds when raw data is copied to prm

NGS_Automated-2.0.12

• added track and trace functionality when all data is copied to prm
• added mailing when sample is rejected
• updated the prm on leucine-zipper

NGS_Automated-2.0.11

bug fix release:

• Rsync group permissions fix
• Changed crontab templates for processing of GenomeScan data by ateambot user as opposed to dm user.
• Removed notifications for analysis step not performed in genomescan group.
• Added log output also to ${JOB_CONTROLE_FILE_BASE}.[started|finished|failed], so it will be picked up by notifications.sh as body for email messages.