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Merge pull request #86 from hydra-genetics/release-v0.1.0
chore: release 0.1.0
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| # Changelog | ||
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| ## 0.1.0 (2022-10-14) | ||
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| ### Features | ||
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| * Add 3 rules for pindel plus envs and script ([5c51855](https://www.github.com/hydra-genetics/cnv_sv/commit/5c5185593b7718fa49270f017bd26e33f63b1243)) | ||
| * add conventional-prs workflow ([94cc587](https://www.github.com/hydra-genetics/cnv_sv/commit/94cc5875c86cd2cdce2dc43a2a2cf4792337811c)) | ||
| * add exomedepth ([ebfe037](https://www.github.com/hydra-genetics/cnv_sv/commit/ebfe037a87564692ee89be8e7114ddc959a6a4d3)) | ||
| * Add logging and make script testable ([167a148](https://www.github.com/hydra-genetics/cnv_sv/commit/167a148bcf91823bbf0cde5f720bfb0c54c8fb7c)) | ||
| * add missing entry in schema ([61a7055](https://www.github.com/hydra-genetics/cnv_sv/commit/61a70557f910f60ef3b9d7a4802f194c33f62cbb)) | ||
| * Add rule cnvkit_call_loh which adapt calls according to TC ([3837d51](https://www.github.com/hydra-genetics/cnv_sv/commit/3837d51dfd94e11f4617fb7c5e887ea595376998)) | ||
| * Add rule to generate cnvkit diagram ([bef8828](https://www.github.com/hydra-genetics/cnv_sv/commit/bef8828521497758e3c9f685dda009c6ca10a721)) | ||
| * added bedfile to pindel call ([36aca30](https://www.github.com/hydra-genetics/cnv_sv/commit/36aca300ac068610384c0534bfe618b64d66aa5b)) | ||
| * Added environments ([c919fed](https://www.github.com/hydra-genetics/cnv_sv/commit/c919fedec6e2b1601c8740fdbae8b178907a57ac)) | ||
| * Added manta rules ([e77071d](https://www.github.com/hydra-genetics/cnv_sv/commit/e77071d8a702e85af9fcc73025bdc7bae29c7ba0)) | ||
| * Added rule cnvkit coverage ([7162e00](https://www.github.com/hydra-genetics/cnv_sv/commit/7162e0084526b6782f986087f7ca5d735857a062)) | ||
| * Added rule cnvkit_call together with test files ([4d7c808](https://www.github.com/hydra-genetics/cnv_sv/commit/4d7c80838866c49cd9dd33ffe124cd09df57e334)) | ||
| * Added rule cnvkit_create_access ([7d5a550](https://www.github.com/hydra-genetics/cnv_sv/commit/7d5a550606a2f8134bf347e7b7ebca31a35bd887)) | ||
| * Added rule cnvkit_create_antitargets ([5fd5d12](https://www.github.com/hydra-genetics/cnv_sv/commit/5fd5d12ea96a4f220823b93e233fa0ed9904ca4a)) | ||
| * Added rule cnvkit_create_targets ([cdb3f5e](https://www.github.com/hydra-genetics/cnv_sv/commit/cdb3f5e14cd0de28173e48a2ebff8ff2a0ef3d8b)) | ||
| * Added rule for manta tumor only calling. Refactor of old rule ([530a295](https://www.github.com/hydra-genetics/cnv_sv/commit/530a29503eecabc46fc814c7eb031fc0db6bb467)) | ||
| * Added rule GATK_cnv_collectAllelicCounts ([d4abf5e](https://www.github.com/hydra-genetics/cnv_sv/commit/d4abf5ed996794397ee24cd3abd0640549e54d3b)) | ||
| * Added rule GATK_cnv_collectReadCounts ([66ab8f7](https://www.github.com/hydra-genetics/cnv_sv/commit/66ab8f7e1163723f0fee38bab1c7ccc8d1befda4)) | ||
| * Added rule GATK_cnv_denoiseReadCounts ([99822b5](https://www.github.com/hydra-genetics/cnv_sv/commit/99822b57882a5b17bdadae43d31445f279598371)) | ||
| * Added rule GATK_cnv_modelSegments ([8c88d06](https://www.github.com/hydra-genetics/cnv_sv/commit/8c88d06e8d210117f2e38e6f7759d94332a1a9fc)) | ||
| * Added rule germline_vcf ([9bbabc4](https://www.github.com/hydra-genetics/cnv_sv/commit/9bbabc42345a7cf416c2fc292287c213987611b8)) | ||
| * Changed cnvkit_vcf to own script ([db9a85d](https://www.github.com/hydra-genetics/cnv_sv/commit/db9a85d03ba086ac4650f163d935e9640369abb8)) | ||
| * Generate output list programmatically ([ef95803](https://www.github.com/hydra-genetics/cnv_sv/commit/ef9580374e6b9b72549183b37f8d3742f8b68e94)) | ||
| * germline vcf now performed by filter vcf using pipeline config and override in Snakemake ([0a427b6](https://www.github.com/hydra-genetics/cnv_sv/commit/0a427b605f4ce1eea3fa8d8b0f1ff4dfcf3b8b80)) | ||
| * make config.yaml location more flexible ([f6f4416](https://www.github.com/hydra-genetics/cnv_sv/commit/f6f4416ec0594aaa92e681266fa33085a095127d)) | ||
| * make configfile/confgilefiles argument mandatory ([02b4f25](https://www.github.com/hydra-genetics/cnv_sv/commit/02b4f25baa9dfd27cfcbbc19a6b6fe293c1962ad)) | ||
| * make module compatible with latest version of snv_indels and alignment module. ([8ea6383](https://www.github.com/hydra-genetics/cnv_sv/commit/8ea638395a2fbed2d8814747b748ca4766bbf4e6)) | ||
| * make output more configurable ([dbd9bbf](https://www.github.com/hydra-genetics/cnv_sv/commit/dbd9bbf3b32aaa2f22f265dc5df22fffee5e214a)) | ||
| * Make unnecessary manta output vcfs temp ([46688c2](https://www.github.com/hydra-genetics/cnv_sv/commit/46688c2a213415323142d439a7908acc3fa67390)) | ||
| * **manta:** added extra params to manta ([e99460f](https://www.github.com/hydra-genetics/cnv_sv/commit/e99460f224c86057478ffb1f8fcdda30b5577926)) | ||
| * new rule cnvkit_vcf that exports segment files to vcf ([9769357](https://www.github.com/hydra-genetics/cnv_sv/commit/976935749710ddcadb0da0385f02351716f98eac)) | ||
| * New rule svdb ([e7349b4](https://www.github.com/hydra-genetics/cnv_sv/commit/e7349b4417a833876576a32a1fc1030257e9487e)) | ||
| * Prepare pindel config script for unit testing ([13b0264](https://www.github.com/hydra-genetics/cnv_sv/commit/13b02646689787c6c34151e3822a0ae8749cbc8f)) | ||
| * setup integration test for exomedepth ([7a30fc0](https://www.github.com/hydra-genetics/cnv_sv/commit/7a30fc0697bc401aa5e63b5f12e733d01a835d77)) | ||
| * update snakemake-version ([830124c](https://www.github.com/hydra-genetics/cnv_sv/commit/830124cb81318ec9eb631806b4e82b5e0ea5af4b)) | ||
| * update svdb version ([d6745f6](https://www.github.com/hydra-genetics/cnv_sv/commit/d6745f65ae7b84182af5a5f5e4aeca12f4590392)) | ||
| * Upgrade pindel to wrapper v85.0.1 ([9048434](https://www.github.com/hydra-genetics/cnv_sv/commit/9048434f3c08f9db153e26e67702d3c63bacb2d5)) | ||
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| ### Bug Fixes | ||
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| * add containers and change from bcftools view to zcat in rule germinline_vcf ([5fa941f](https://www.github.com/hydra-genetics/cnv_sv/commit/5fa941f7aa8f34492a712bece844e725b727d177)) | ||
| * add contigs to pindel-vcf ([4a52b00](https://www.github.com/hydra-genetics/cnv_sv/commit/4a52b0038e18c2301e80106eec4017e5b4a6cf3f)) | ||
| * add library to install for exomedepth ([63d19c2](https://www.github.com/hydra-genetics/cnv_sv/commit/63d19c221ff679f7dda47976dee62a965ca2fdec)) | ||
| * Added resources, rule name fix, rm testfiles, rm wp1 in config ([f408a14](https://www.github.com/hydra-genetics/cnv_sv/commit/f408a14af5893ae2e034a29cfb3d7b75a62fa448)) | ||
| * better vcf annotation for filtering ([8aa6da8](https://www.github.com/hydra-genetics/cnv_sv/commit/8aa6da8bed5b35d88c86cb45809c2ef92996d445)) | ||
| * bugfix ([140842c](https://www.github.com/hydra-genetics/cnv_sv/commit/140842c587a64e7b25183c0b58ad67b903a850b0)) | ||
| * change run column name to flowcell in units. ([a69af37](https://www.github.com/hydra-genetics/cnv_sv/commit/a69af37ad1759e8e155527655d056e399494e7b6)) | ||
| * change TC to tumor_content ([8c11ee6](https://www.github.com/hydra-genetics/cnv_sv/commit/8c11ee695e48331bd9a829b4e6808129eea67457)) | ||
| * change to point to master ([41e6d16](https://www.github.com/hydra-genetics/cnv_sv/commit/41e6d166dddcd5d0bccdbaabb7b42b81ca981079)) | ||
| * change type from float to number ([1731573](https://www.github.com/hydra-genetics/cnv_sv/commit/1731573fb98df66c6eb497bbc5851a1b82632521)) | ||
| * Changed name again ([ea530f1](https://www.github.com/hydra-genetics/cnv_sv/commit/ea530f1c59da79dc95b71721d907e5247ea33c23)) | ||
| * **cnvkit:** change python version ([f315187](https://www.github.com/hydra-genetics/cnv_sv/commit/f31518771ec929884e222977b5d7e31a50e72374)) | ||
| * **cnvkit:** change to correct conda env file ([be3d3ba](https://www.github.com/hydra-genetics/cnv_sv/commit/be3d3ba5d3a9bca28daa23031f93684723182608)) | ||
| * Correct runWorkflow script path and add container to config ([057b151](https://www.github.com/hydra-genetics/cnv_sv/commit/057b1511bf66fe80acb0dc0ceba34233c208477c)) | ||
| * don't install snakemake using mamba ([dc08143](https://www.github.com/hydra-genetics/cnv_sv/commit/dc08143c1c088d91d8b09a46c92029e846fd56fe)) | ||
| * float in header ([4e30d39](https://www.github.com/hydra-genetics/cnv_sv/commit/4e30d39b5470061211cbc1577722a797381a0f03)) | ||
| * float in header ([7c0c233](https://www.github.com/hydra-genetics/cnv_sv/commit/7c0c23333eed9a0f1d5779d150445c8add3c9d7d)) | ||
| * handling of multiple databases ([978d218](https://www.github.com/hydra-genetics/cnv_sv/commit/978d2185aa2a0a0c9b282ee6099872577ceb9ba2)) | ||
| * info ids to long ([541bd8d](https://www.github.com/hydra-genetics/cnv_sv/commit/541bd8d4e8df4566872e82ed7b475482900370d0)) | ||
| * int to float in vcf headers ([331da1d](https://www.github.com/hydra-genetics/cnv_sv/commit/331da1d554ecddec9c5e5be2f328a097020a9308)) | ||
| * lock singularity version to prevent bug with latest version ([bfe978e](https://www.github.com/hydra-genetics/cnv_sv/commit/bfe978ea5e29d00fd6835e23b090f5eb5020d877)) | ||
| * reference under rule ([92fd035](https://www.github.com/hydra-genetics/cnv_sv/commit/92fd03538d20ae7043606fd3f8594f77f3ddcec4)) | ||
| * remove unused dependency. ([81f7ed6](https://www.github.com/hydra-genetics/cnv_sv/commit/81f7ed66695ed3a472bad33c6b5646dee25eb27c)) | ||
| * revert changes ([e74b497](https://www.github.com/hydra-genetics/cnv_sv/commit/e74b497594df70e11e881f95c169d958fc740432)) | ||
| * rule name change ([f617b06](https://www.github.com/hydra-genetics/cnv_sv/commit/f617b0655fe332b359407f7c3ed357a68e222d5c)) | ||
| * set correct env file ([c81d30d](https://www.github.com/hydra-genetics/cnv_sv/commit/c81d30de64d4cc291e32b270c3a8a763c10d7fa5)) | ||
| * set strict mode for conda ([d070bda](https://www.github.com/hydra-genetics/cnv_sv/commit/d070bdab490f726339e5a03263e674dd67b58612)) | ||
| * update r script to handle empty results ([6bd463b](https://www.github.com/hydra-genetics/cnv_sv/commit/6bd463b141a14ba16669f59b816ad49b7580824f)) | ||
| * used corrected cn instead of cn ([dc59207](https://www.github.com/hydra-genetics/cnv_sv/commit/dc5920740d9cc54f12e73ca5390fb096f2d2f2a8)) | ||
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| ### Documentation | ||
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| * add and fix schema for picard_update_vcf_sequence_dictionary ([9bba1e9](https://www.github.com/hydra-genetics/cnv_sv/commit/9bba1e9cb72bf3b0c3e966006e61372b3bb6971a)) | ||
| * add configfile option to example ([da7ff6b](https://www.github.com/hydra-genetics/cnv_sv/commit/da7ff6b239181bf9ac13cae94a68c7fe93045220)) | ||
| * add description to all config- and resources-schemas ([d7103d4](https://www.github.com/hydra-genetics/cnv_sv/commit/d7103d40fbfa5c102dfcc7b27fcba50e4c29e2eb)) |