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CHANGELOG.md

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nf-core/aquascope: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

dev

v3.0.0

Added/Fixed

  • Feature docs by @arunbodd in CDCgov#56
  • NF-core template update, added three new entry points by @slsevilla in CDCgov#60
  • Added CI workflow to test the pipeline by @antongray1 in CDCgov#62
  • Updated FREYJA version by @slsevilla in 7d615c8b9bf33272025d0ded0770ed7650db287a
  • Update schema requirrements by @slsevilla in f98393af109e5ff9592dff27b449eaf982f899b1
  • Fix samplesheet col name inconsistency by @slsevilla in 2a511d6b013aa67262363669169d33e3c5abd5d1

Docs

  • Updated readme to trigger mkdocs workflow by @antongray1 in CDCgov#65

Depreciated

  • Removed redundant code by @slsevilla in f879ac397a3b13fd6136e01fa04f9ed119b3094f
  • Removed IVAR Variant calling in c01698754e10d63af4b700f4feacfb1ed701fcbb
  • Removed Samtools FAIDX by @slsevilla in c8163ad7c419570da881153ca90dd5d435a6ac03

v2.3.1

Added

added awk to assign gff_feature to freyja - variant calls by @arunbodd in #53

v2.3.0

Added

chore: remove conflicting code by @arunbodd in #51 Add test profile for ONT data, add test data, update configs, cleanup gitignore files by @slsevilla in #49 Rebase dev from testprofiles, add new config by @arunbodd in #50 Rebasing dev to main after issues with previous merge by @slsevilla in #52

v2.2.0

Added

Merge pull request #40 from CDCgov/dev by @arunbodd in #47

Fixed

Re: Reheader Bam issue addressed by @arunbodd in #40 Update images, samplesheet updates, rehead BAM by @slsevilla in #45

v2.1.0

Added

  • Feature Add: Amino Acid calling, threshold features added #27 by @arunbodd @schavan023 in #31

Docs

  • Updated README and user-docs by @slsevilla @arunbodd in #29, #30, #33

v2.0

Added

  • 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.
  • 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.
  • 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)
  • ci: added github actions for deployment

Fixed

  • Hseabolt patch 1 by @slsevilla in #25
  • fix: removed ivar trim which was erroring for ONT-long reads
  • fix: Removed parameter --fai (fasta index), it now builds using samtools faidx

Docs

  • Update README.md by @SMorrison42 in #12
  • Docs Overhaul, CI addition, IVAR feat add by @slsevilla in #21
  • docs: updated README
  • docs: update CHANGELOG format
  • docs: created a VERSION log

Deprecated

v1.0dev - [date]

  • Initial release of nf-core/aquascope, created with the nf-core template.