diff --git a/CHANGELOG.md b/CHANGELOG.md index a0f77a4f82..3b80cfcdf6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,18 +9,28 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added -- [#353](https://github.com/nf-core/sarek/pull/353) - Add support for task retries with exit code 247 (exhibited by Picard MarkDuplicates) +- [#353](https://github.com/nf-core/sarek/pull/353) - Add support for task retries with exit code 247 (exhibited by `Picard MarkDuplicates`) +- [#354](https://github.com/nf-core/sarek/pull/354) - Add tumor only mode for `Mutect2` and `MSIsensor` +- [#356](https://github.com/nf-core/sarek/pull/356) - Add `--cf_contamination_adjustment` params to adjust contamination with `Control-FREEC` +- [#372](https://github.com/nf-core/sarek/pull/372) - Add `--cf_contamination` params to specify contamination value with `Control-FREEC` ### Changed -- [#333](https://github.com/nf-core/sarek/pull/333) - Bump `Sarek` version to `3.0dev` +- [#373](https://github.com/nf-core/sarek/pull/373) - Sync `TEMPLATE` with `tools` 1.14 +- [#376](https://github.com/nf-core/sarek/pull/376) - Better logo on Github dark Mode +- [#383](https://github.com/nf-core/sarek/pull/383) - Update CHANGELOG ### Fixed +- [#375](https://github.com/nf-core/sarek/pull/375), [#381](https://github.com/nf-core/sarek/pull/381), [#382](https://github.com/nf-core/sarek/pull/382) - Fix bugs due to `TEMPLATE` sync from [#373](https://github.com/nf-core/sarek/pull/373) +- [#378](https://github.com/nf-core/sarek/pull/378) - Fix `Spark` related issue due to `Docker` settings in `nextflow.config` + ### Deprecated ### Removed +- [#368](https://github.com/nf-core/sarek/pull/368) - Remove social preview image to use GitHub OpenGraph + ## [2.7](https://github.com/nf-core/sarek/releases/tag/2.7) - Pårte Pårte is one of the main massif in the Sarek National Park.