2.0.0-rc1

What's Changed

• Updates Cycas to 0.6.1, with a new algorithm to form and calibrate consensus based on read structure type classifications
• Updates workflow to new metadata, adding and adjusting report plots to include read structure type information
• Changes variant filtering minimum ABQ to 20, roughly adjusted for new calibrated qualities
• Removes variant filters for orientation ratio, because new consensus forces reads into forward orientations
• Updates variant effect prediction annotations to include codon and aminoacid changes, remove irrelevant annotations from report table, parse for readability
• Adds major updates to reporting: now using plotly and Jinja2 for plots and report
• Removes tab and card with deprecated information (removed backbone-related sections)
• Updated container to use micromamba base image and only bioconda and conda-forge channels

Full changelog since last release: 1.1.3..2.0.0-rc1