-
Notifications
You must be signed in to change notification settings - Fork 2
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #72 from hydra-genetics/release-v0.1.0
chore: release 0.1.0
- Loading branch information
Showing
1 changed file
with
50 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| # Changelog | ||
|
|
||
| ## 0.1.0 (2022-04-20) | ||
|
|
||
|
|
||
| ### Features | ||
|
|
||
| * add compatibility test against alignment module." ([7237bf0](https://www.github.com/hydra-genetics/snv_indels/commit/7237bf09705c7507ebc06fd149727f866746e04d)) | ||
| * add conventional-prs workflow ([ceba918](https://www.github.com/hydra-genetics/snv_indels/commit/ceba918d775b9ffe8e81a03e2ff12108aa0e0b35)) | ||
| * Add logging, refactor and fix some bugs ([8c5c09f](https://www.github.com/hydra-genetics/snv_indels/commit/8c5c09f8363d0cfc9af3e76e2b5daf379f8395d7)) | ||
| * add pull-request template ([14250d1](https://www.github.com/hydra-genetics/snv_indels/commit/14250d1ac84ee7e2afc514f770082fce9bd87bbb)) | ||
| * add resources to rules. ([d1a0efd](https://www.github.com/hydra-genetics/snv_indels/commit/d1a0efdd97ec02391def69066e7a4fb651900ea4)) | ||
| * Add tabix indexing rule. Also adapted merg_vcf to take indexed vcf as input. ([a27cb03](https://www.github.com/hydra-genetics/snv_indels/commit/a27cb03ac1b864a8a9fc62d974f903ce1cbb0b68)) | ||
| * added annotate rule ([601c698](https://www.github.com/hydra-genetics/snv_indels/commit/601c698829f1fd124244c0e1ec163c597428d4ef)) | ||
| * Added decompose, normalize and sort of vcf files ([69a14b7](https://www.github.com/hydra-genetics/snv_indels/commit/69a14b7bb323bbbd857c4b9232861a9b16ad1219)) | ||
| * added release-please workflow ([8e171e1](https://www.github.com/hydra-genetics/snv_indels/commit/8e171e1d87b2e600e7679381412acb3e8301d9eb)) | ||
| * Added rule ensemble_vcf (bcbio recall). Also made sort_vcf more general. ([4d6464c](https://www.github.com/hydra-genetics/snv_indels/commit/4d6464c3a8fd205802a0a0ca1770358d318b3cbc)) | ||
| * Match rules to standard, optimize, add functions ([c3185f9](https://www.github.com/hydra-genetics/snv_indels/commit/c3185f9f3b4adda639771c29373c6b62782d3ec4)) | ||
| * moved rule: filter_vcf_on_format move to filtering module ([ebd1f41](https://www.github.com/hydra-genetics/snv_indels/commit/ebd1f41fd54e91e8e27a8759d560993d3f668c52)) | ||
| * moved rule: filter_vcf_on_format move to filtering module ([3e3207e](https://www.github.com/hydra-genetics/snv_indels/commit/3e3207e4a8cc7793578cd646dd62216afe120f04)) | ||
| * mutect2 rule ([202e7c2](https://www.github.com/hydra-genetics/snv_indels/commit/202e7c2303764da41c336d6e372a6705a456d663)) | ||
| * new rule bed_split. Changed reference and bam files ([cf9dcd7](https://www.github.com/hydra-genetics/snv_indels/commit/cf9dcd72e5f69fa6609ef86038d077989e55172d)) | ||
| * New rule bgzip for vcf-files ([3ab1abd](https://www.github.com/hydra-genetics/snv_indels/commit/3ab1abd14f4aa23e9596dc5c588379afe5dd68be)) | ||
| * New rule merge vcf ([0f275ba](https://www.github.com/hydra-genetics/snv_indels/commit/0f275ba331cb975a2c44864533d53d238948ba02)) | ||
| * New rule mutect2_gvcf that generates a gvcf instead of vcf ([0e1abcc](https://www.github.com/hydra-genetics/snv_indels/commit/0e1abccf58250e4267f0b792c707af5cc5bce6ed)) | ||
| * New rule: fixAF ([bdd4efd](https://www.github.com/hydra-genetics/snv_indels/commit/bdd4efded783d0d5cdc758e774eb5eb480c4282d)) | ||
| * New rule: merge_gvcf ([cf250cd](https://www.github.com/hydra-genetics/snv_indels/commit/cf250cda317010e19873302fa016679e0dbd405c)) | ||
| * New vardict rule ([517129f](https://www.github.com/hydra-genetics/snv_indels/commit/517129f36059fdd78ea02b004abc8111d10f5e58)) | ||
| * Remove snver, fix error message ([0ed6b16](https://www.github.com/hydra-genetics/snv_indels/commit/0ed6b16f59e082232887d88f0b315cb40be49be1)) | ||
| * Rule for filtering of vcf files. Also added env for conda. ([1566924](https://www.github.com/hydra-genetics/snv_indels/commit/15669247e622438e3362011522fde4a70d149375)) | ||
| * update version of common container ([52b7b6b](https://www.github.com/hydra-genetics/snv_indels/commit/52b7b6b86d5b60dd776d6486e7b975a6fdf6671b)) | ||
| * Use barcode as part of units index and set wildcard constr ([d52c2cd](https://www.github.com/hydra-genetics/snv_indels/commit/d52c2cd4b62499d593d07a291571d3fa7a26d027)) | ||
| * Use g.vcf extension for gvcf files ([eacc3a3](https://www.github.com/hydra-genetics/snv_indels/commit/eacc3a3606b846b6e91dd81b29ec81649511ad1c)) | ||
|
|
||
|
|
||
| ### Bug Fixes | ||
|
|
||
| * Added bam-index as input to vardict ([4c6d72b](https://www.github.com/hydra-genetics/snv_indels/commit/4c6d72b61100cabc73f8cfca523ef60c7665a131)) | ||
| * change run column name to flowcell in units. ([5385f22](https://www.github.com/hydra-genetics/snv_indels/commit/5385f226d758de6c6fa773caa90b1164ef7162f7)) | ||
| * Downgrade conda package versions to avoid crash ([061365a](https://www.github.com/hydra-genetics/snv_indels/commit/061365a9746dac670d4b085576950537bb1f93a2)) | ||
| * fixed bam location based on alignment prep-release ([d08edb3](https://www.github.com/hydra-genetics/snv_indels/commit/d08edb374b8eeca48d0870cce212e28328bf69fb)) | ||
| * lock singularity to version that works with our images from dockerhub ([5115f39](https://www.github.com/hydra-genetics/snv_indels/commit/5115f3905da86e48ba9fb0f760a0693328b38c27)) | ||
| * Vardict skips reads with mapq 0. Also, correct columns in bed file as default ([72be218](https://www.github.com/hydra-genetics/snv_indels/commit/72be2184629e4d5266714540145a25c929dbb1d3)) | ||
|
|
||
|
|
||
| ### Documentation | ||
|
|
||
| * Add latest rule graph ([037d108](https://www.github.com/hydra-genetics/snv_indels/commit/037d108866d5224b30fbd97c0388666cfb626624)) | ||
| * update pull-request template ([79f7cfb](https://www.github.com/hydra-genetics/snv_indels/commit/79f7cfb4bf2fff00d020b113eae8f717dee07061)) | ||
| * Update README ([4a237f0](https://www.github.com/hydra-genetics/snv_indels/commit/4a237f0f2aee97995dfc782d608794e24ac494cc)) |