v1.1.1

1.1.1 (2024-11-04)

Bug Fixes

• fix file not found error on shared fs storage (#673) (c28db96)

v1.1.0

1.1.0 (2024-10-31)

Features

• FLiRT Mutations column (#664) (f77d42e)

Bug Fixes

• changed kraken input files for ont (#650) (b62007c)
• move primer file location under workflow; this avoids file not being found in shared filesystems (#665) (9cb1576)
• pangolin data updates (#662) (f46ec83)
• replace ragoo with ragtag (#591) (e64e9db)

v1.0.0

1.0.0 (2024-04-17)

Bug Fixes

• docs deployment (#635) (dd767b0)
• more meaningful info for patient overview table (#609) (77f7960)
• pin to varlociraptor 8.4.4 (#634) (a4e1ea8)
• pipe of stdout (#631) (a48a357)
• remove -r flag (#624) (4f1b56b)
• update link for covariants (#626) (e6476b6)

Miscellaneous Chores

• release 1.0.0 (07d6fe2)

v0.16.0

0.16.0 (2023-11-16)

Features

• Update README.md for dark/light theme (#614) (33ac5f7)

Bug Fixes

• changes in path requirements for snakedeploy (#590) (406d456)
• improved clonality event definition, usage of major subclone for assembly polishing; upgrade to varlociraptor 6.0 (#585) (aced95e)
• QA genome generation (#613) (2bb74bf)
• switch from jupyter notebook to script (#598) (d0f293d)
• update multiqc (#607) (0070d89)
• use homopolymer-pair-HMM-mode of Varlociraptor in case of nanopore reads (505a271)
• use homopolymer-pair-HMM-mode of Varlociraptor in case of nanopore reads (#587) (9bc814f)

Performance Improvements

• update to varlociraptor 8.4 (#596) (34701af)

v0.15.1

0.15.1 (2022-11-30)

Bug Fixes

• ci: update black to rev 22.3.0 (#523) (2273b7d)
• disable ont actions (#555) (56e46ef)
• Replace outdated df append (#544) (4a40003)
• update channel priorities and snakemake wrappers (#562) (a0b6fd0)
• use latest varlociraptor release and ignore all biases in case of known lineage variant calling (#575) (fa957fd)
• voc probability (#541) (db6eb17)

v0.15.0

0.15.0 (2022-03-24)

Features

• update rbt to 0.39 (#510) (91b5ac5)

Bug Fixes

• add nofilter flag for variant calls (#505) (381007c)
• primer clipping add up- and downstream (#515) (5c886fa)

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)

v0.13.2: chore(master): release 0.13.2 (#442)

0.13.2 (2022-01-06)

Bug Fixes

• wrong enumeration with kallisto included (#439) (1a68969)

v0.13.1: chore(master): release 0.13.1 (#440)

0.13.1 (2022-01-04)

Bug Fixes

• relative aggregation sample plot (#412) (6a8155e)

v0.13.0: chore(master): release 0.13.0 (#438)

0.13.0 (2022-01-03)

Features

• add optional column for adapters (#419) (f883ce2)
• add patient or environmental mode flag (#420) (9ac2002)
• add prettier to pre-commit (#427) (e7cb0a7)

Bug Fixes

• generate high quality report .csv file (#433) (077b80d)