v0.14.0

0.14.0 (2022-03-21)

Features

• add variant call details based on protein annotation (#487) (016bcfb)
• call known lineage variants (#392) (9ad720c)
• deps: bump github/super-linter from 4.8.6 to 4.8.7 (#459) (c18f241)
• deps: update pangolin to 3.1.19 (#461) (3971687)
• deps: update pangolin to 3.1.19 (#461) (d5f42ca)
• deps: update pangolin to 3.1.20 (#467) (78cb7f4)
• make incoming and archive structure data-handling optional (#443) (559e9c1)
• make sending lab column in rki report csv adjustable via config file (#492) (311e857)
• rule and script bed_to_bedpe (#447) (3022eab)

Bug Fixes

• add missing fasta index to vcf report (#480) (1697fb5)
• add missing voc variant report to environmental report (#479) (16baef1)
• bump rust-bio-tools to 0.38 (#449) (e85fa15)
• canu and porechop logging (5db0935)
• canu and porechop logs (#473) (497bfcd)
• ci: add missing missing echo to release please (#476) (6a0b899)
• ci: change human reference from NC_000021.9 to BA000005.3 (#488) (14b4be0)
• ci: change release please PR branch (#481) (603d3b5)
• ci: parse new json output from release please (#474) (eb598b7)
• ci: release please checkout branch (#477) (03a69bf)
• correct filtering in plot-lineages-over-time (#445) (c71f72b)
• deps: update multiqc wrapper (#329) (42fbcd8)
• fixed include flag KeyError (#452) (f47dad2)
• order of include flag sample (#462) (429e5d9)
• pangolin plot color (#483) (9e368d5)
• reduce loading time of coverage plots (#498) (8a8f533)
• remove removal of .indicators/replacement_notice.txt for int (#457) (c5b9f6c)
• rename column header in report formatter (#444) (8ba21d9)
• reset over table formatter (#448) (ee30a46)
• untmp recalibrated bam (#491) (1118fd9)
• VOC mutation table similarity calculation (#484) (82405ee)

Performance Improvements

• add ont temp flags (#475) (6447583)
• ont downsampling normalisation (#489) (f502dd2)
• optimisations for ont - barcode+adapter-trimming, primer-trimming (porechop) and read correction (Canu) (#454) (e844fc4)