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Update changelog #326

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Jan 20, 2021
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Update changelog #326

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8998cd9
fix: change link to bio.tools from old to new id
maxulysse Jan 19, 2021
7a867f6
update CHANGELOG
maxulysse Jan 19, 2021
23cc4a5
chores: Update CHANGELOG.md
maxulysse Jan 19, 2021
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2 changes: 1 addition & 1 deletion .github/RELEASE_CHECKLIST.md
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Expand Up @@ -27,7 +27,7 @@
7. Wait for reviews
8. Merge said PR
9. Make a [release](https://github.com/nf-core/sarek/releases) on GitHub
10. Update [bio.tools](https://bio.tools/Sarek) with the new release details
10. Update [bio.tools](https://bio.tools/nf-core-sarek) with the new release details
11. RT the nf-core automated tweet about the new released version
12. Make a new branch from `dev`
13. Checkout the `CHANGELOG.md` from `master`
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24 changes: 17 additions & 7 deletions CHANGELOG.md
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Expand Up @@ -9,18 +9,23 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Added

- [#230](https://github.com/nf-core/sarek/pull/230) - Add `ignore_soft_clipped_bases` option for `GATK Mutect2` [#218](https://github.com/nf-core/sarek/issues/218)
- [#145](https://github.com/nf-core/sarek/pull/145) - Add `UMI annotation and consensus` functionality to `Sarek`
- [#230](https://github.com/nf-core/sarek/pull/230) - Add `ignore_soft_clipped_bases` option for `GATK Mutect2` [#218](https://github.com/nf-core/sarek/issues/218)
- [#253](https://github.com/nf-core/sarek/pull/253) - Add `UMI` `CI` testing
- [#262](https://github.com/nf-core/sarek/pull/262) - Add `nextflow_schema.json`
- [#237](https://github.com/nf-core/sarek/pull/237), [#282](https://github.com/nf-core/sarek/pull/282) - Add `--aligner` to choose between `bwa` and `bwa-mem2`
- [#294](https://github.com/nf-core/sarek/pull/294) - Add `Troubleshooting` section to `docs/usage.md`
- [#302](https://github.com/nf-core/sarek/pull/302), [#304](https://github.com/nf-core/sarek/pull/304) - Add WES and tumor-only mode for `Control-FREEC`

### Changed

- [#237](https://github.com/nf-core/sarek/pull/237) - Switch `bwa 0.7.17` for `bwa-mem2 2.0`
- [#253](https://github.com/nf-core/sarek/pull/253), [#255](https://github.com/nf-core/sarek/pull/255) - Update docs
- [#260](https://github.com/nf-core/sarek/pull/260), [#262](https://github.com/nf-core/sarek/pull/262), [#278](https://github.com/nf-core/sarek/pull/278) - Sync with `TEMPLATE` updated from [nf-core/tools](https://github.com/nf-core/tools) [`1.10.2`](https://github.com/nf-core/tools/releases/tag/1.10.2)
- [#253](https://github.com/nf-core/sarek/pull/253), [#255](https://github.com/nf-core/sarek/pull/255), [#326](https://github.com/nf-core/sarek/pull/326) - Update docs
- [#260](https://github.com/nf-core/sarek/pull/260), [#262](https://github.com/nf-core/sarek/pull/262), [#278](https://github.com/nf-core/sarek/pull/278), [#322](https://github.com/nf-core/sarek/pull/322) - Sync with `TEMPLATE` updated from [nf-core/tools](https://github.com/nf-core/tools) [`1.10.2`](https://github.com/nf-core/tools/releases/tag/1.10.2)
- [#262](https://github.com/nf-core/sarek/pull/262) - Update issue templates to fit the recommended community standards
- [#278](https://github.com/nf-core/sarek/pull/278) - Refactor docs
- [#278](https://github.com/nf-core/sarek/pull/278), [#322](https://github.com/nf-core/sarek/pull/322) - Refactor docs
- [#284](https://github.com/nf-core/sarek/pull/284) - Update F1000Research publication to version 2
- [#284](https://github.com/nf-core/sarek/pull/284) - Update Scilifelab logo
- [#317](https://github.com/nf-core/sarek/pull/317) - Update `README.md` (Add: QBiC + Friederike/Gisela)

### Fixed

Expand All @@ -30,15 +35,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#272](https://github.com/nf-core/sarek/pull/272) - Fix annotation `--tools merge` issue
- [#279](https://github.com/nf-core/sarek/pull/279) - Fix issue with `--step prepare_recalibration` [#267](https://github.com/nf-core/sarek/issues/267)
- [#280](https://github.com/nf-core/sarek/pull/280) - Use HTML codes instead of `<` and `>` in docs
- [#288](https://github.com/nf-core/sarek/pull/288) - Fix `test_annotation` profile
- [#289](https://github.com/nf-core/sarek/pull/289) - Random string added to `extractFastqFromDir` to avoid name collition
- [#290](https://github.com/nf-core/sarek/pull/290), [#323](https://github.com/nf-core/sarek/pull/323) - Faster solving of `Conda` environment
- [#293](https://github.com/nf-core/sarek/pull/293) - Fix typo issue when printing infos [#292](https://github.com/nf-core/sarek/issues/292)
- [#309](https://github.com/nf-core/sarek/pull/309) - Fixed concatenation of many VCF files
- Fix Github Actions not running after November 16, 2020 (deprecated Github Actions API [#739](https://github.com/nf-core/tools/issues/739)
- [#310](https://github.com/nf-core/sarek/pull/310) - Fix Github Actions not running after November 16, 2020 (deprecated Github Actions API [#739](https://github.com/nf-core/tools/issues/739)

### Removed

- [#234](https://github.com/nf-core/sarek/pull/243) - Removing obsolete script [#92](https://github.com/nf-core/sarek/issues/92)
- [#262](https://github.com/nf-core/sarek/pull/262) - Removing warning message about deprecated and obsolete params
- [#262](https://github.com/nf-core/sarek/pull/262) - Removing deprecated params: `annotateTools`, `annotateVCF`, `cadd_InDels`, `cadd_InDels_tbi`, `cadd_WG_SNVs`, `cadd_WG_SNVs_tbi`, `maxMultiqcEmailFileSize`, `noGVCF`, `noReports`, `noStrelkaBP`, `nucleotidesPerSecond`, `publishDirMode`, `sample`, `sampleDir`, `saveGenomeIndex`, `skipQC`, `snpEff_cache`, `targetBed`
- [#262](https://github.com/nf-core/sarek/pull/262) - Removing warning message about deprecated and obsolete params
- [#324](https://github.com/nf-core/sarek/pull/324) - `--no_gatk_spark` is now removed, use `--use_gatk_spark` instead
- [#324](https://github.com/nf-core/sarek/pull/324) - `--no_gvcf` is now removed, use `--generate_gvcf` instead

## [2.6.1](https://github.com/nf-core/sarek/releases/tag/2.6.1) - Gådokgaskatjåhkkå

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