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