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v1.5.3
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@kevinlibuit kevinlibuit released this 15 Sep 03:08
· 135 commits to main since this release
v1.5.3
87ca249

Patch to address vulnerability in Mercury Prep workflows to the inadvertent removal of internal Ns when preparing assemblies for GenBank submission
This patch replaces the sed one liner that removed leading N's from assembly files in preparation for GenBank submission with the NCBI fasta-trim-terminal-ambigs.pl script as the sed solution was found to be vulnerable to inadvertent removal of non-terminal Ns in multi-line assembly files.

Other modifications made

  • NextClade default image updated to v1.3.0; nextclade_one_sample task modified to accommodate changes in sourcing reference files
  • GISAID metadata passage_history field auto-populated as original in the Mercury Prep workflows--other required fields (patient_age, patient_gender, and patient_status) populated as unknown if no input value is provided
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