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@DarianHole DarianHole released this 06 Jun 20:06
0.2.0-dev
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v0.2.0-dev - [2025-06-06]

Dev release of all of the nextflow code and updates to the pipeline. All of the Illumina processing should be working well! The nanopore processing side still needs a bit more to match the illumina which is why it is a dev release

Added

  • All of the pipeline has been rewritten in Nextflow
  • Illumina paired-end sequencing workflow added
    • Freebayes for variant calling over ivar variants/consensus previously
  • Nanopore (initial) workflow added
    • clair3
  • DSId assignment added when using --dsid fasta parameter
    • Based on full sequence match
  • Summary outputs added
    • Amplicon summary report
    • The current Rmarkdown report needs to be fixed for the new outputs
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