3.10.20231115

Minor update:

• updates freyja container to 1.4.7-2023-11-14
• adds heatcluster and phytreeviz when --relatedness true

3.9.20231107

Minor release:

• Updates freyja to version 1.4.7-2023-11-07

3.9.20231102

Minor release (unless you use Freyja boot):

• due to the length of time it takes Freyja boot to run, Freyja boot has been dropped from the workflow. If this feature is of interest to you, please submit an issue and freyja boot can be added back in future release with conditional operation.
  • correspondingly, params.freyja_boot_options has also been dropped as it is no longer used.
  • the 'freyja' process has been divided into two processes : 'freyja variants' and 'freyja demix'
  • the default value of params.freyja_plot_options = '--mincov 100' has reverted back to params.freyja_plot_options = ''

3.8.20231031

Minor release:

• update freyja to 1.4.7-2023-10-31
• update pangolin to 4.3.1-pdata-1.23.1
• update included SARS-CoV-3 nextclade dataset to 2023-10-26T12:00:00Z (use by setting params.download_nextclade_dataset = false)
• fix ivar log files in multiqc

3.8.20231024

Minor update:

• Update freyja to 1.4.7-2023-10-24
• Update artic to 1.2.4-1.11.1

3.8.20231017

Minor Update:

• updated Freyja to 1.4.7-2023-10-17

3.8.20231010

Minor release:

• updates nextclade SARS-CoV-2 database (use by setting params.download_nextclade_dataset = false)
• updates freyja to 1.4.7-2023-10-10

3.8.20231003

Minor update

• updates Freyja to 1.4.7-2023-10-03

3.8.20230926

Minor release

• updated included nextclade dataset (released last week)
  • use by setting params.download_nextclade_dataset = false

Unless you consider how Cecret uses Freyja

• Freyja has been updated to use UPHL's 1.4.7-2023-09-26 container

• Updated default values for Freyja-related params to take minimum_depth into consideration (we were hopeful this would speed up the workflow)

  • current Freyja-related defaults:
    • params.minimum_depth = 100 (unchanged - it is still used for ivar_variants, bcftools_variants, and ivar_consensus)
    • params.freyja_aggregate_options = "" (unchanged)
    • params.freyja_boot_options = "--nb 1000 --depthcutoff ${params.minimum_depth}" (changed from "--nb 1000")
    • params.freyja_demix_options = "--depthcutoff ${params.minimum_depth}" (changed from "")
    • params.freyja_plot_filetype = "png" (unchanged)
    • params.freyja_plot_options = "--mincov ${params.minimum_depth}" (changed from "")
    • params.freyja_variants_options = "" (unchanged)

  Please submit an issue if you run into problems!

3.8.20230915

Moderate release:

• added midnight primers (midnight idt version 1, midnight ont versions 1-3)
  • added information to readme at https://github.com/UPHL-BioNGS/Cecret#determining-primer-and-amplicon-bedfiles
• GA test for primers
  • setting vadr to false for some GA tests (still too large in most cases)
• adjusted ampliconstats defaults
• downgraded samtools to 1.17
• upgraded freyja to 1.4.7-20230915
• changed artic container to 1.2.4-1.9.4-1 because of dependencies