2.0.2021115

This update introduces:

• profiles
  • instead of forcing the end user to link to a config file, there are now profiles to choose from. Also, this workflow no longer need to be downloaded from git first. The new recommended usage is

  nextflow run UPHL-BioNGS/Cecret -profile singularity
  

• nextclade has been updated to use --datasets
• nextalign is now an option for multiple sequence alignment instead of mafft (specify params.relatedness = true and params.msa = 'nextalign')
• Cecret_annotation.nf has been removed. Instead, just put fastas into the main workflow by putting them in the same directory.
• Removed fastq files and instead suggests using https://github.com/CDCgov/datasets-sars-cov-2. The summary files from this dataset are now all that is included in the data subdirectory.
• This is a new version because some of the params have changed and may not be backward compatible
• The default depth is now 100X (up from 10X). This can be adjusted back down to 10X by the end user by specifying params.minimum_depth = 10