Merge pull request #27 from jlanga/release-please--branches--master

chore(master): release 1.1.0

Author: jlanga

CHANGELOG.md

@@ -0,0 +1,62 @@
+# Changelog
+
+## [1.1.0](https://github.com/jlanga/smsk_popoolation/compare/v1.0.0...v1.1.0) (2024-04-26)
+
+
+### Features
+
+* add hp ([2f35806](https://github.com/jlanga/smsk_popoolation/commit/2f3580639ce06b2b42917efae87381d20a7c7aee))
+* bwa -> bwa-mem2 ([c06521e](https://github.com/jlanga/smsk_popoolation/commit/c06521ee16610edf9f5fa142fc032f177b387d43))
+* clean popoolation functions ([bc34d29](https://github.com/jlanga/smsk_popoolation/commit/bc34d2949ed237b09903892e192be1dd583b7f02))
+* clean preprocess ([954e417](https://github.com/jlanga/smsk_popoolation/commit/954e417ea3a0d33fa73ce62635304979ed77e9ae))
+* clean up reads ([4fe9e6d](https://github.com/jlanga/smsk_popoolation/commit/4fe9e6dfb608ff314fde7e3b5a92b11d1344ef73))
+* clean up report ([9acfcc0](https://github.com/jlanga/smsk_popoolation/commit/9acfcc07f58938e9a822d7e492cc6e35a1d8dee8))
+* cleaning up ([b65999d](https://github.com/jlanga/smsk_popoolation/commit/b65999de22e4b4179abe42c368ca92906e51bb1b))
+* cleanup ([17bcf28](https://github.com/jlanga/smsk_popoolation/commit/17bcf280c1ba98204e9f9b1e026fae45f73744b7))
+* compute coverage from pileups ([126895f](https://github.com/jlanga/smsk_popoolation/commit/126895f741d9475701196ccc5476c4938f43f074))
+* disable all protected ([662c6cc](https://github.com/jlanga/smsk_popoolation/commit/662c6cca35087d176fbd2f9574ee20c2d1885818))
+* extract helpers ([840651c](https://github.com/jlanga/smsk_popoolation/commit/840651c0bbc9aef60305c554be0ef2a21b7ad324))
+* extract popoolation1 and popoolation2. not tested ([6056753](https://github.com/jlanga/smsk_popoolation/commit/605675335f5c3ec30c3bf362c327f4e48d5096fb))
+* extract preprocess ([f76e4d0](https://github.com/jlanga/smsk_popoolation/commit/f76e4d0e3e00f496ea35b9fa335dfa232e6e0438))
+* extract reads ([9107ceb](https://github.com/jlanga/smsk_popoolation/commit/9107ceb690183ff9041535f294beff59a7a80183))
+* extract reference. Use custom reference name ([eea30c3](https://github.com/jlanga/smsk_popoolation/commit/eea30c34ba7f035f7ae72c741b5d19caf0a92f49))
+* handle dots in the chromosomes ([8498cad](https://github.com/jlanga/smsk_popoolation/commit/8498cad66347e34b939a4f85c0557ba1da1af225))
+* in popoolation2, write population names rather than numbers ([ee0b0a3](https://github.com/jlanga/smsk_popoolation/commit/ee0b0a3ddf44e43a52cb591d2f91cc8c08d277ab))
+* leave only coreutils ([e493f48](https://github.com/jlanga/smsk_popoolation/commit/e493f489c1486aadc9f274016c69063ef41aa630))
+* lint popoolation1 and 2 ([d6910a0](https://github.com/jlanga/smsk_popoolation/commit/d6910a06f384ab465bd8ddb0debc0082e18fb86b))
+* lint R code ([b2adead](https://github.com/jlanga/smsk_popoolation/commit/b2adeadcad012f05f555b2b8fd25bc4212a77a2d))
+* multiple window and step sizes in popoolation1 ([9be9332](https://github.com/jlanga/smsk_popoolation/commit/9be933255e532bd9cfb244d8fc34fdd5b50c43ff))
+* multiple window and step sizes in popoolation2 ([953a880](https://github.com/jlanga/smsk_popoolation/commit/953a8801eec302045b96a746b540668bbf514aa0))
+* parse units, capture stdout to log ([49a3f35](https://github.com/jlanga/smsk_popoolation/commit/49a3f35c3c69aebe6aaa31552280dd82a89b68a5))
+* plot coverage ([d5e6327](https://github.com/jlanga/smsk_popoolation/commit/d5e6327a46cdd1d84751b6d223dfefde85e130ea))
+* put hp in its place ([453cd09](https://github.com/jlanga/smsk_popoolation/commit/453cd099cd449a8ee45b483cbb6e003e965e95e4))
+* put popoolation in its place. add reports ([6228cfe](https://github.com/jlanga/smsk_popoolation/commit/6228cfe9369566112cbe651f7c0760de8cf809c4))
+* refactor ([968dd57](https://github.com/jlanga/smsk_popoolation/commit/968dd5780a4a431c0242217af0feb86e60dd33a1))
+* refactor get_files ([ab7d366](https://github.com/jlanga/smsk_popoolation/commit/ab7d366be0c29fcad390d06cc725457ce8906170))
+* remove extras ([98957ea](https://github.com/jlanga/smsk_popoolation/commit/98957ea391678a57cba2beeb5b2f8c20af7cc1f0))
+* remove gzip dependency. use bgzip instead. use default level ([8ca05a7](https://github.com/jlanga/smsk_popoolation/commit/8ca05a758d1cf7d40df4a30b287fe4a5af447e29))
+* remove numpy dependency. update envs ([dd9ce40](https://github.com/jlanga/smsk_popoolation/commit/dd9ce402409bc9642bb1024ae7f69eae90f86114))
+* remove version from popoolation ([93a7edd](https://github.com/jlanga/smsk_popoolation/commit/93a7edd6530d072fd5c3c2556bc3304e0e19ca12))
+* reorder population and chromosome file structure ([868be53](https://github.com/jlanga/smsk_popoolation/commit/868be5326fdb3e8b639035cf74e2fd7e35d7a1df))
+* restyle popoolation ([7154aea](https://github.com/jlanga/smsk_popoolation/commit/7154aea4e281c934f022def32073bab857f01543))
+* separate the mpileup column joining into a script ([c967226](https://github.com/jlanga/smsk_popoolation/commit/c967226e9ce3748a61c91404b73e93765dcf6ec3))
+* simplify ([7998886](https://github.com/jlanga/smsk_popoolation/commit/7998886f7f175882dd13b42a290d4115b2c026eb))
+* snakefmt ([fa0058a](https://github.com/jlanga/smsk_popoolation/commit/fa0058a027be30fc78ab64077f734a4481682fae))
+* split rmdup and filter. update envs ([22e0803](https://github.com/jlanga/smsk_popoolation/commit/22e0803ec2843485da277f57d484912e11800f78))
+* update envs ([4396634](https://github.com/jlanga/smsk_popoolation/commit/43966349e82228e008a5a84463a241ba588a02d3))
+* use default samtools compression. remove unnecessary sort ([2a7ada5](https://github.com/jlanga/smsk_popoolation/commit/2a7ada5527ee50d0d6056f63382a825667814776))
+
+
+### Bug Fixes
+
+* don't ask in target rules for nontarget files ([e5bd3fb](https://github.com/jlanga/smsk_popoolation/commit/e5bd3fb93c313469453b2eab5abf24099dbddd92))
+* don't keep uncompressed outputs ([48320b9](https://github.com/jlanga/smsk_popoolation/commit/48320b964304651def3aab0cb203090440deb402))
+* folder name ([8ede5cd](https://github.com/jlanga/smsk_popoolation/commit/8ede5cd8d1605d2032ac296dd951c899f124fe07))
+* handle dots in the references ([540fb97](https://github.com/jlanga/smsk_popoolation/commit/540fb9753d20a2ed67b98c8a75e19ea1dee46008))
+* manage properly bwamem2 indexes ([6f585f0](https://github.com/jlanga/smsk_popoolation/commit/6f585f0214f0dd6a60e91dd00945a1a6926b3c77))
+* merge conflict ([0dfc78d](https://github.com/jlanga/smsk_popoolation/commit/0dfc78d3492bf4cbc08211b10a4380671d8fc581))
+* run gha on main, master and devel, just in case ([4c74cb9](https://github.com/jlanga/smsk_popoolation/commit/4c74cb97216d3b5ade95f2383267483c229f7485))
+* show badge in readme, disable all-temp in CI ([5b035cd](https://github.com/jlanga/smsk_popoolation/commit/5b035cd8c198d720de8263feabd4bfdcfd06718e))
+* simpler sample job ([aaf249b](https://github.com/jlanga/smsk_popoolation/commit/aaf249b1b770d839477bcfdfead240d1b22a74ca))
+* sort populations and libraries to avoid pop2_vs_pop1 ([480fb46](https://github.com/jlanga/smsk_popoolation/commit/480fb46a2e8bf03b4c11bdd5cc49822ad6e0d844))
+* trimmomatic ([f047d0c](https://github.com/jlanga/smsk_popoolation/commit/f047d0c4d23eb80ca4664842a7b8f64ba19db3fa))