Merge pull request #2 from RIVM-bioinformatics/release-please--branch…

…es--main--components--juno_variant_typing

chore(main): release 0.1.0

CHANGELOG.md

@@ -0,0 +1,52 @@
+# Changelog
+
+## 0.1.0 (2024-03-18)
+
+
+### Features
+
+* add consensus generation ([037d125](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/037d12503b4f30dab8380323827eeb5d1533e3ed))
+* add manual version checks ([1577530](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/15775308830f71f4cfd40979541669869dd9bff3))
+* add mtb lineage type as prototype ([f9f1273](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/f9f12734c88fafe961f479b4c53a36ac1eb204ea))
+* add parsing of snpeff to variant table ([4cb2cbf](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/4cb2cbfad34f9922ecc4de9adf8056421799f572))
+* add presets ([8c5309d](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/8c5309da7cb8c3d3a8a88c0e68d07f242be35c50))
+* add small test dataset based on K1F phage ([d4a3bdb](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/d4a3bdbd0e468c0fa3a8eb1b6ca392a177d72ad0))
+* add snpeff annotation ([a2123fa](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/a2123fa2e960bd36d95666d6249d0f53d732929f))
+* copy and prepare input files ([4d98315](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/4d9831570368b1ccf1a5f5fa8d346c232bf9124f))
+* include unfiltered variants in tsv output ([5832b92](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/5832b924543482ebce00e3e3b0625a89c287eb71))
+* produce tb sequence experiment json for database ([502fc57](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/502fc57f6121795116ef8f281b99c5417f7b83cf))
+
+
+### Bug Fixes
+
+* add data to coll positions bed ([9765610](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/97656103e6ad09afa90dbb9ee719fa49e7fc4e04))
+* add helper scripts for variant annotation ([88605d4](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/88605d42a80b9493ee52d474ded2083cf1425e93))
+* add rrs and rrl count to output ([794a7a9](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/794a7a9ef25969e88a058e158f4053b71f1655df))
+* bind db dir in wrapper ([df1c0c8](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/df1c0c81f790fdbb3487c2587e009e03105e8568))
+* correct path to db ([2ac4337](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/2ac433798cfb19d2835273684dd3977c0d8e4e7c))
+* correct path to resistance list on biogrid ([aea4ead](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/aea4ead9e82567857bc69ea1277f69b971e0dbfd))
+* count only filtered variants in defined regions ([c7aa626](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/c7aa6268f316fd510bea8255e0c154f24857dba8))
+* first conversion of template to jvt ([3b5d02d](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/3b5d02d91185aa4c84d7abb7999925c607ed6e60))
+* fix error when no typing needed ([152bbc7](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/152bbc7bcce3d00c110195fa02e9711f6bd547d3))
+* fix filtering for resistance mutations ([7d61cff](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/7d61cff7f6be8fa63ea90b23c89e3d9a9769f82c))
+* fix mypy typing error ([e8f5118](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/e8f511838836cc7de2a2c94f5087c690fdaf9fe7))
+* make column names more informative ([62ca364](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/62ca3640b750343865847b730dcac936befe6ef4))
+* python executable name for container ([85a8ad2](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/85a8ad204d9f1fa3681387bd98653b947a6fd4cb))
+* snpeff executable ([294eff7](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/294eff7eb9fe96dda18cf6188467b36741d39090))
+* snpeff executable name ([2b9af66](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/2b9af669d2b71b5c0ad22d20c624890de35a4b66))
+* sync conda and sing versions ([e82a948](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/e82a9487efa770d4dc5192178cc85f6a9be9020c))
+* treat ref and allele columns as non-VCF compliant ([0e6a956](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/0e6a956b45db013b1cf954dd7e6ca706bff5f7ba))
+* typo in default arg ([200210b](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/200210b03b02f25f40f2e5ed1415795879060b58))
+* update typing ([06482cd](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/06482cd61df329cdb105f7617addb61f1e105020))
+
+
+### Dependencies
+
+* add conda envs ([5d2bb78](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/5d2bb78e8113b5f33a7eb748db9e8e350403b475))
+* add containers ([d9d4f5e](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/d9d4f5e53ef38ef3214bc0e820e48db19f0a3a41))
+* remove anaconda ([ca745ec](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/ca745eccc49d2c67b02af02bff411cfef989a5fc))
+* set correct container ([cef23c4](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/cef23c413871466bee26ea0b1306022dc82783ad))
+* sync conda install with containers ([f9a8d6b](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/f9a8d6b795ff8d1dab7e0ed14a6e64e0bf93a3a0))
+* update library version ([8c23189](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/8c2318985437c5ef7ffd2b2de4f170f43ca9b6a2))
+* upgrade snakemake and juno-lib ([cd94fed](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/cd94fed336197172a6555998d8ad41c237dc6168))
+* use smk v7.24 to prevent reinstall with pip ([fca70fb](https://github.com/RIVM-bioinformatics/juno-variant-typing/commit/fca70fb59ed7be760cd098ebaefae71463bb18f9))

version.py

@@ -2,5 +2,5 @@
 __authors__ = "Boas van der Putten"
 __email__ = "[email protected]"
 __license__ = "AGPLv3"
-__version__ = "0.0.1"
+__version__ = "0.1.0"
 __description__ = "Juno variant typing pipeline for interpretation of genomic variants"