3.11.20240123

Minor update

• updates Freyja to 1.4.8-2024-01-23
• updates pangolin to 4.3.1-pdata-1.24

3.11.20240116

Moderate update:

• update nextclade to version 3.0.0
  • remove nextalign multiple sequence alignment option - well, replaced it with nextclade, but all nodes are included
• update included SARS-CoV-2 nextclade dataset (use by setting params.download_nextclade_dataset = false)
• separate aci to run per sample instead of per run
• update samtools and bcftools to 1.19
• update aci to 1.4.20240116
• update freyja to 1.4.8-2024-01-16
• update vadr to 1.6.3

3.10.20240109

Minor Release:

• Updates Heatcluster to 1.0.2c
• Updates Freyja to 1.4.8-2024-01-09

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