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@j3551ca j3551ca released this 27 Dec 22:38
· 11 commits to main since this release
v2.0.1
d275756
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Learn about vigilant mode.

  • Change errorStrategy to 'ignore' all failures on Freyja demix (lineage_freyja) process, not only negative control samples

  • Change errorStrategy to 'retry' twice on SnpEff (annotate_snpeff) process in case it is the first time pipeline is being run. SnpEff database needs to be downloaded and the first time will download but fail, then because it is now present rerunning will work.

  • Adjust QC align commands to be more informative (samtools coverage and depth).

  • Add trace file to track samples (that fail lineage_freyja process).

  • Reuse ref_ch defined in treatment workflow for effluent

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