3.25.24353

Minor release:

• Update freyja to 1.5.2-12_15_2024-01-38-2024-12-16

3.25.24348

Bug fixes:

• freyja aggregate (#396)
• samtools_plot_ampliconstats, multiqc, fastqc, param toggles (#394)

3.22.24346

Adjusted glob for input paired-end fastq files from directory. (Fixes #394)

3.22.24345

• changes default primer set to ncov_V5.3.2
• updates freyja to 1.5.2-12_08_2024-01-33-2024-12-09
• updates minimum nextflow version
• fixes paths in GA

3.22.24331

Moderate release:

• Used nf-tools to create new nextflow_schema.json

  • the devs still can't test it, so submit an issue if it isn't working

• Updated processes

  • freyja to 1.5.2-12_08_2024-01-33-2024-12-09
  • updated samtools/bcftools to 1.21
  • updated bwa to 0.7.18
  • updated bbtools to 39.10
  • updated iqtree2 to 2.3.6
  • updated mafft to 7.526

• In the backend:

  • renamed all processes to uppercaps
  • separated CECRET into the workflow directory
  • created INITIALIZE subworkflow
  • updated tests
  • created modules config files

No longer working (will be returned soon):

• using user supplied zipped nextclade datasets
• using nextclade for multiple sequence alignment
• getting a copy of the config file with --config_files

3.15.24324

Minor release:

• Updates freyja to 1.5.2-11_18_2024-01-35-2024-11-18
• Updates included SARS-CoV-2 nextclade dataset (use by setting params.download_nextclade_dataset = false)

3.15.24310

Minor update:

• updates freyja to 1.5.2-11_04_2024-01-48-2024-11-04

3.15.24303

Minor update:

• update freyja to 1.5.2
• update nextclade to 3.9.1

3.15.24296

Minor release (with bug fix):

• Nanopore reads with a sample sheet should be fixed (#375)
• Updates nextclade to 3.9.0
• Updates included SARS-CoV-2 nextclade dataset (use by setting params.download_nextclade_dataset = false)

3.15.24275

Minor release:

• Updates pangolin to 4.3.1-pdata-1.30
• Updates freyja to 1.5.1-09_30_2024-01-39-2024-10-01
• Updates included SARS-CoV-2 nextclade dataset (use by setting params.download_nextclade_dataset = false)