3.10.20240103

Minor Update:

• Update freyja to 1.4.8-2024-01-02

3.10.20231226

Minor release:

• updated freyja to 1.4.8-2023-12-26
• changed freyja_demix_options default to " "
• update included SARS-CoV-2 nextclade dataset (use by setting params.download_nextclade_dataset = false)
• updated heatcluster to 1.0.2b-2023-12-26 and fixed sorted_matrix.csv file location.
• added igv reports

3.10.20231219

Minor release:

• update artic to for latest version of medaka (artic version 1.2.4 ; medaka version 1.11.3)
• all seaborn containers have changed to pandas containers
• update freyja to 1.4.8-2023-12-19
• update heatcluster to 1.0.2
• update multiqc to 1.19

3.10.20231212

Minor release:

• adds pango collapse (pango collapse traces pangolin lineages to their Delta parent lineage) for SARS-CoV-2 samples
• updates artic container to 1.2.4-1.11.3-2023-12-12 for new medaka version
• updates freyja container to 1.4.8-2023-12-12
• adds text to readme

3.10.20231205

Minor release (unless running into issues with singularity and pangolin) with mostly version bumps:

• update included SARS-CoV-2 nextclade dataset (use by setting params.download_nextclade_dataset = false)
• updated freyja to 1.4.7-2023-12-05
• updated artic to 1.2.4-1.11.2-2023-12-05 for medaka version 1.11.2
• updated heatcluster to 0.4.13-2023-12-05
• changed phytreeviz container to staphb from uphl
• updated pangolin to 4.3.1-pdata-1.23.1-1 (which should resolve issues like #258 and has the latest version of usher)

3.10.20231128

Minor release:

• updates nextclade SARS-CoV-2 database (use by setting params.download_nextclade_dataset = false)
• updates freyja to 1.4.7-2023-11-28

3.10.20231121

Minor release:

• updates samtools to 1.18
• updates freyja to 1.4.7-2023-11-21

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 = ''