1.4.0 include LCS lineage read screening

What's Changed

• included LCS pooled sample implementation by @hoelzer and @replikation in #216
  • can be activated via --screen_reads
  • can take approx. 4-5 h per sample! so make sure you have a cluster/cloud to distribute the workload
• bumping the default nextclade and pangolin containers
• updated kraken2 database via @oliverdrechsel for read classification closes #178

Full Changelog: 1.3.0...1.4.0

improved report

What's Changed

Improvements made by @RaverJay to improve the readability of the HTML report

• Report VOCs, VOIs in the final report by @RaverJay in #206
• Table style updates by @RaverJay in #213

Full Changelog: 1.2.1...1.3.0

update on varskip2 primer

What's Changed

• VarskipV2, pool fix and consistent ordering by @bwlang in #212
• updated help and readme to better understand how to provide custom primer bed files @replikation

New Contributors

• @bwlang made their first contribution in #212

Full Changelog: 1.2.0...1.2.1

1.2.0

What's Changed

• seqrs V4.1 support and singularity envWhitelist by @MarieLataretu in #208
• Custom bed file input by @replikation in #211
• provide your own bed files via ``--primerV ownprimerfile.bed`
  • documentation will be added soon for this. make sure your bed file follows the same artic primer rules with naming etc.
• working primer support for VarSkipV2

Full Changelog: 1.1.0...1.2.0

1.1.0

What's Changed

• adding VarSkip2 primer by @replikation in #203
• Report command line by @RaverJay in #197
• Bump Medaka version in ARTIC container by @hoelzer in #196
• Use nextclade aa insertions by @RaverJay in #198
• add frameshift column by @RaverJay in #205
• Bump default Pangolin and Nextclade container

Full Changelog: 1.0.0...1.1.0

1.0.0

• added mid barcode detection, slightly increases overall read number after demultiplexing
• VarSkip primer added
• ARTIC 4.1 primer set added (omicron support)
• disabled guppy pings to avoid errors in some cases
• insertion are now added to the report
• gzip FASTA support
• default pangolin and nextclade container are up. (we still recommend using the --update flag for the most recent definitions)

0.11.7

Quick fix for reporting amino acid insertions in the report: Nextclade changed the index and thus we needed to adjust the translation of insertions reported on nucleotide level in Nexclade to insertions on amino acid level for the report.

0.11.6

Add support for the ARTIC V4.1 primer kit for better recovery of Omicron sequences.

0.11.5

• small update especially for basecalling on a SLURM system
• also disable Guppy pings in case of firewalls blocking the signal and thus causing basecalling to fail

0.11.4

• add insertions to the report
  • this is done currently via translating nt insertions reported by Nextclade into aa insertions to show them in the report, e.g. for Omicron
• add information about scorpio and scorpio constellation files to the report, also put other important tool versions more prominent on top of the report
• allow gzip FASTA input
• bumps up default version of Pangolin and Nextclade to new ones