CHANGELOG.md

Changelog

1.1.1 (2024-11-04)

Bug Fixes

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

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)

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)

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)

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• Replace outdated df append (#544) (4a40003)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)

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)

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)

0.13.2 (2022-01-06)

Bug Fixes

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

0.13.1 (2022-01-04)

Bug Fixes

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

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)

0.12.0 (2021-12-23)

Features

• add varlociraptor test case generation (#429) (3ec7975)

Bug Fixes

• update the mutations columns in the overview table formatter (#423) (3af43b9)

0.11.0 (2021-12-21)

Features

• update to rust-bio-tools 0.33 (#388) (8f66915)
• update to varlociraptor 4.9 (#424) (5a7ca5b)

0.10.2 (2021-12-19)

Bug Fixes

• pangolin input for overview table, bamclipper samtools error, include flag for high quality genome report (#418) (9690f12)

0.10.1 (2021-12-17)

Bug Fixes

• names in report (#410) (e5dbcbd)

0.10.0 (2021-12-16)

Features

• complete workflow if no samples pass the quality filter (#411) (55b2dcc)

0.9.0 (2021-12-15)

Features

• added variants-over-time-plot to report again (#405) (bd5048a)

0.8.0 (2021-12-15)

Features

• add pangolin call table (#397) (953211a)
• add rki include/exclude flag (#319) (d2e6d20)
• added column in overview table for the clear name of the lineage (#400) (38e34bb)

Bug Fixes

• change report structure, add masked sequence, pangolin call on polished sequence (#396) (d2ecaaa)
• rmv pipe from pre-commit (#401) (3222bb2)

0.7.0 (2021-12-14)

Features

• add pre commit checks (#398) (6982b3d)

Bug Fixes

• remove cwd-check in update sample sheet script (#393) (44d49d3)
• trigger docs build on release created (#391) (e240aeb)

0.6.0 (2021-12-13)

Features

• update pangolin to 3.1.17 (#389) (23ed39e)
• update varlociraptor to version 4.8 (#331) (0096376)

Bug Fixes

• generation of high quality genomes (#394) (da00975)
• relative aggregation of samples for variants and lineages over time plots (#382) (ebe556c)

0.5.0 (2021-12-09)

Features

• technology: add ion torrent processing (#383) (288777c)

0.4.1 (2021-12-07)

Bug Fixes

• ci: adjust commit message of copyright-preamble.yml to fit conventional commits format (#369) (e067895)
• GISAID lineage extraction [B.1.1.529 (probably).fasta] (#372) (7750862)

0.4.0 (2021-12-02)

Features

• technology: add Oxford Nanopore processing (#305) (55f38f3)

Bug Fixes

• add bam index for extract_reads_of_interest (#366) (5f5dd27)
• changed contigs file for quast-rule to avoid workflow to stop because of low read numbers (#338) (2d0e246)
• changed JSON schema validator and updated files #364 (75e62f2)

Performance Improvements

• changed chunksize of read json file from gisaid, excluded lineage without name (#328) (b9e5c49)

0.3.1 (2021-11-29)

Bug Fixes

• nested function usage and remove code duplication (#323) (91e3ce9)

0.3.0 (2021-11-05)

Features

• add aggregation rule for publication plots (#275) (a93bc18)
• add more voc mutations to config (#314) (5098605)
• add plot of reads needed for sufficient lineage calling (#263) (982f997)
• add plot of variants over time (#279) (66ab121)
• add schemes for sample sheet and config file (#278) (09976b3)
• add standard reference lineages for kallisto based lineage calling (#280) (6bb32f6)
• add todo action (#277) (c1e44c5)
• add workflow catalog yml (#199) (2013533)
• comparison of assemblers (#172) (8233829)

Bug Fixes

• add "snakemake" in the readme for the Snakemake Workflow Catalog requirements (#309) (2e5212c)
• changed call config file in update-sample-sheet (#307) (406aef7)
• shotgun typo in config.yaml (#308) (d30f02b)
• specify snakemake version used in pangolin env (#284) (79a12a8)

0.2.5 (2021-09-23)

Bug Fixes

• sha tag name (#273) (b6d1265)

0.2.4 (2021-09-23)

Bug Fixes

• add log in to quay registry (#271) (16080de)

0.2.3 (2021-09-23)

Bug Fixes

• update readme to trigger release (#269) (19129a9)

0.2.2 (2021-09-22)

Bug Fixes

• rmv path for buildah (#265) (2341a61)

0.2.1 (2021-09-22)

Bug Fixes

• container version tag (#262) (d4c1ef6)

0.2.0 (2021-09-22)

Features

• adding new rule update_sample to workflow (#254) (3878c1b)

Bug Fixes

• maximize build space for container image (#261) (0de2cc9)

0.1.8 (2021-09-20)

Bug Fixes

• add missing path to the Dockerfile job (#258) (e733d2d)

0.1.7 (2021-09-20)

Bug Fixes

• update snakemake actions for container file (#256) (cb31e92)

0.1.6 (2021-09-16)

Bug Fixes

• change path of docker file (#251) (1abebcf)

0.1.5 (2021-09-15)

Bug Fixes

• add GISAID var to env (#248) (e859aed)

0.1.4 (2021-09-14)

Bug Fixes

• change " to ' (#246) (ffca497)

0.1.3 (2021-09-09)

Bug Fixes

• add extract gisaid env (#235) (2b94752)
• improve if statement with release check (#239) (12cc85f)

0.1.2 (2021-09-06)

Bug Fixes

• merge push to quay.io into release please (#231) (e9d782d)
• remove pre von relase action (#232) (301043f)

0.1.1 (2021-09-01)

Bug Fixes

• change trigger of registry release action (#223) (1464ece)

0.1.0 (2021-08-31)

Bug Fixes

• change release-please-action (#217) (20af1db)
• change trigger of release please (#212) (c7a9978)
• relase plase indent (#216) (9140a29)
• release command (#219) (fb84404)
• release please command (#218) (7c64689)
• release please if statement (#220) (41f41d5)
• release please local PR checkout (#221) (b348aa7)
• release please pr tag (#215) (5d54bb4)
• release please rmv double dollar (#222) (0003da9)
• release please step id (#214) (fa5a9cc)

Miscellaneous Chores

• release 0.1.0 (#201) (f211058)