diff --git a/CHANGELOG.md b/CHANGELOG.md index 8c2fa9b77..811235113 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,9 +7,24 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Credits +Special thanks to the following for their contributions to the release: + +- [Adam Talbot](https://github.com/adamrtalbot) +- [Edmund Miller](https://github.com/edmundmiller) +- [Jonathan Manning](https://github.com/pinin4fjords) +- [Laramie Lindsey](https://github.com/laramiellindsey) +- [Matthias Zepper](https://github.com/MatthiasZepper) +- [Maxime Garcia](https://github.com/maxulysse) +- [Rob Syme](https://github.com/robsyme) +- [Thomas Danhorn](https://github.com/tdanhorn) + +Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. + ### Enhancements & fixes - [PR #1186](https://github.com/nf-core/rnaseq/pull/1186) - Properly update qualimap/rnaseq module (ie not patch) +- [PR #1197](https://github.com/nf-core/rnaseq/pull/1197) - Delete lib directory and replace with utils\_\* subworkflows +- [PR #1199](https://github.com/nf-core/rnaseq/pull/1199) - Replace modules.config with more modular config files per module/subworkflow/workflow - [PR #1201](https://github.com/nf-core/rnaseq/pull/1201) - Template update for nf-core/tools v2.12 - [PR #1206](https://github.com/nf-core/rnaseq/pull/1206) - Remove `lib/` directory and `modules.config` - [PR #1210](https://github.com/nf-core/rnaseq/pull/1210) - Use pseudoalignment subworkflow components from nf-core/modules @@ -17,6 +32,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #1213](https://github.com/nf-core/rnaseq/pull/1213) - Pass transcriptome fasta through to samtools stats - [PR #1214](https://github.com/nf-core/rnaseq/pull/1214) - Bump umitools + delocalise prepareforrsem ([#831](https://github.com/nf-core/rnaseq/issues/831)) - [PR #1216](https://github.com/nf-core/rnaseq/pull/1216) - Delocalise catadditionalfasta ([#1162](https://github.com/nf-core/rnaseq/issues/1162)) +- [PR #1217](https://github.com/nf-core/rnaseq/pull/1217) - Update Emiller88 => edmundmiller in README - [PR #1218](https://github.com/nf-core/rnaseq/pull/1218) - Template update for nf-core/tools v2.13 - [PR #1220](https://github.com/nf-core/rnaseq/pull/1220) - Initialise nf-test and add pipeline level test - [PR #1221](https://github.com/nf-core/rnaseq/pull/1221) - Use nf-test test for all nf-core components @@ -35,8 +51,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #1240](https://github.com/nf-core/rnaseq/pull/1240) - Fix reference files params usage - [PR #1241](https://github.com/nf-core/rnaseq/pull/1241) - Add nf-test tests to deseq2_qc - [PR #1242](https://github.com/nf-core/rnaseq/pull/1242) - Use dupradar from nf-core/modules +- [PR #1243](https://github.com/nf-core/rnaseq/pull/1243) - Add nf-test for module MULTIQC_CUSTOM_BIOTYPE - [PR #1244](https://github.com/nf-core/rnaseq/pull/1244) - Add gtf2bed tests +- [PR #1245](https://github.com/nf-core/rnaseq/pull/1245) - nf test quantify rsem +- [PR #1246](https://github.com/nf-core/rnaseq/pull/1246) - nf-test quantify pseudoalignment +- [PR #1247](https://github.com/nf-core/rnaseq/pull/1247) - nf-test prepare_genome +- [PR #1249](https://github.com/nf-core/rnaseq/pull/1249) - Include nf-tests for rsem_merge_counts module - [PR #1250](https://github.com/nf-core/rnaseq/pull/1250) - Remove all tags.yml files because the testing system has changed +- [PR #1251](https://github.com/nf-core/rnaseq/pull/1251) - Replace deseq2qc paths ### Parameters @@ -48,10 +70,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Dependency | Old version | New version | | ----------- | ----------- | ----------- | +| `bedtools` | 2.30.0 | 2.31.1 | | `multiqc` | 1.20 | 1.21 | | `picard` | 3.0.0 | 3.1.1 | -| `samtools` | 1.17 | 1.18 | +| `samtools` | 1.17 | 1.19.2 | | `sortmerna` | 4.3.4 | 4.3.6 | +| `umi_tools` | 1.14 | 1.15 | > **NB:** Dependency has been **updated** if both old and new version information is present. >