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@RoanKanninga RoanKanninga released this 10 Apr 06:40
· 420 commits to master since this release
3.5.4
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Learn about vigilant mode.

updates:

  • requesting resources for a protocol is now handled via a parameters file (bigger datasets sometimes require more resources). all #MOLGENIS headers are removed from the protocols. This can now be used with the new Molgenis-Compute (see below)

  • reads with a mapping quality below 20 will not be used in calculating coverage

  • new Molgenis-Compute-19.01.1-Java-11.0.2 version (before: Molgenis-Compute-17.08.1-Java-1.8.0_74)

bugfixes:

  • (diagnostics) fixing ONCO_v5 issue. The pipeline will execute genderCheck automatically when there is chrX available. ONCO_v5 has only a very small percentage of targets on chrX which is not reliable enough. fix: when ONCO, no GenderCheck
  • rejected samples (due to no or 0.0% reads for a barcode) were not removed from the samplesheet.
  • Gavin bugfix: when choosing option BOTH the merged INFO fields will be pasted directly to the other INFO fields without a separator, this is now fixed (with perl replace command)
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