Releases · molgenis/NGS_Automated

Minor bug fixes and improved robustness for processing GenomeScan data:

Added -bare suffix for NGS_Automated version number in cron templates.
Added config file for zf-ds.gcc.rug.nl
etc/umcg-genomescan-extend.cfg: Use ${GROUP} var for default group. (Use hardcoded group values only for the exceptions.)
etc/umcg-genomescan.cfg: Updated email notification config to send notifications for state of relevant analysis steps.
processGsRawData.sh:
- Run script as ateambot user without write acces to prm as opposed to dm user with write access to prm.
- Reset *.started files.
- Convert dos/win/mac line end charaters in samplesheets to unix format.
- Remove empty lines from samplesheets.
- Ensure last line in samplesheet contains line end character.

Bugfix for local scope of _checksumVerification variable.
Various bug fixes for error handling.
Use JOB_CONTROLE_FILE_BASE environment variable to create job.failed file when uncaught error is trapped.
- Added export of JOB_CONTROLE_FILE_BASE to scripts in bin/*
- Added option to create ${JOB_CONTROLE_FILE_BASE}.failed in /lib/sharedFunctions.bash
Upgraded ngs-utils to version 18.08.1 for bugfixes in renameFastQs.bash.
Cron jobs:
- Renamed cron job files for umcg-atd-* users to include username.
- Added missing cron jobs for all clusters for atd, gaf and gd groups.
- Switched all cron jobs for the atd group to use a beta version version of NGS_Automated.
- Switched all cron jobs for the gd and gaf groups to use the new 2.0.9 version of NGS_Automated.

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