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@slsevilla slsevilla released this 03 May 03:10
· 254 commits to main since this release
v2.0.0
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What's Changed

  • Update README.md by @SMorrison42 in #12
  • Hseabolt patch 1 by @slsevilla in #25
  • Docs Overhaul, CI addition, IVAR feat add by @slsevilla in #21
  • feat: Added processing of Ion-torrent Bams and ONT long reads
  • feat: Added Nanoplot as Quality metrics tool for ONT long reads
  • feat: Samtools ampliconclip is used as primary trimming tool for ONT-long reads.
  • fix: removed ivar trim which was erroring for ONT-long reads
  • refactor: specify primer bed file as 7th column in samplesheet - refer to ReadME file
  • refactor: Qualimap Bamqc and Ivar variant calling now use "gff" file as one of the parameters, instead of bed or gff3 file formats.
  • fix: Removed parameter --fai (fasta index), it now builds using samtools faidx
  • feat: MultiQC report shows Freyja Demix results.
  • feat: fasta and gff are now defaulted to assets folder. User input required to change these references (We strongly suggest users * * not to use a different reference, as it may lead to accession ID conflicts downstream)
  • docs: updated README
  • docs: update CHANGELOG format
  • docs: created a VERSION log
  • ci: added github actions for deployment

New Contributors

Full Changelog: 1.0.0...v2.0.0

Contributors

slsevilla and SMorrison42
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