NGS_Automated-3.6.0

Feature: Support for GS projects/samples with data from multiple flowcells (in the same batch).

• copyRawDataToPrm.sh:
  • Archive mode will only rsync raw data to prm and disable splitting samplesheets per project.
• Added new copySamplesheetsForBatchToPrm.sh: transfers all project based samplesheets to the location on prm that triggers downstream analysis when all flowcells of a batch were successfully transferred to prm by copyRawDataToPrm.sh

Feature: more fine grained lock files:

• copyRawDataToPrm.sh:
  • Switched from one lock file per group to one lock file per group per combination of ${sourceServer} and ${SCR_ROOT_DIR}.
    This means instances of copyRawDataToPrm.sh for in-house and external sequencing can run simultaneously.

NGS_Automated-3.5.0

• replaced ssh commands in pullRawDataFromDS with rsync commands
• added cfg for lz-ds and zf-ds

NGS_Automated-3.4.0

• added config files for umcg-patho and umcg-labgnkbh
• new script for copying Bcl data directly to prm (copyBclDataToPrm)

NGS_Automated-3.3.0

New

• make symlinks on complementary prm when copying array data prm

bugfixes

• only notify for failed pipelines when they were resubmitted once and failed again
• wrong logging of whether email notifications are enabled or not
• pullRawDataFromDS.sh: do not crash and make sure other batches are processed when a .finished for one batch is not present yet
• only log changes in a project's log dir when something has changed for that specific project
• continue with separate converted GS samplesheet as opposed to using in place conversion, which may get lost due to rsync from data staging server while processing is ongoing
• no cleanup of data on the staging machine in genomescan testgroup
• fixed no emailing of failed genomescan runs

NGS_Automated-3.2.0

Merge pull request #192 from RoanKanninga/master

bugfixes + added track and trace to processGSRawData

NGS_Automated-3.1.0

• added arrayConversion for the GSA/GAP pipeline
• track and trace via notifications

NGS_Automated-3.0.3

• Bugfix: run01.copyRawDataToPrm.finished is now touched when all the array glaasjes are done or when the data of filePrefix is finished
• bugfix: when there is no barcode in the vcf file (old data) then barcode=""
• bugfix: concordanceMakeSamplesheet is not giving an error when there is no barcode

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)