Update Changelog

Author: egreenberg7

CHANGELOG.md

@@ -3,7 +3,44 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v3.15.0dev - [date]
+## v3.16.0dev - [date]
+
+Special thanks to the following for their contributions to the release:
+
+Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
+
+### Enhancements & fixes
+
+- [PR #1351](https://github.com/nf-core/rnaseq/pull/1351) - Adding Kraken2/Bracken on unaligned reads as an additional quality control step to detect sample contamination
+
+### Parameters
+| Old parameter      | New parameter               |
+| ------------------ | `--contaminant_screening`   |
+|                    | `--kraken_db`               |
+|                    | `--save_kraken_assignments` |
+|                    | `--save_kraken_unassigned`  |
+|                    | `--bracken_precision`       |
+
+> **NB:** Parameter has been **updated** if both old and new parameter information is present.
+> **NB:** Parameter has been **added** if just the new parameter information is present.
+> **NB:** Parameter has been **removed** if new parameter information isn't present.
+
+### Software dependencies
+
+| Dependency     | Old version | New version |
+| -------------- | ----------- | ----------- |
+| `Kraken2`      | ----------- | 2.1.3       |
+| `Bracken`      | ----------- | 2.9         |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
+
+### Credits
+
+## [[3.15.0](https://github.com/nf-core/rnaseq/releases/tag/3.15.0)] - 2024-09-04
 
 ### Credits
 
@@ -17,14 +54,15 @@ Special thanks to the following for their contributions to the release:
 - [Luke Zappia](https://github.com/lazappi)
 - [Matthias Zepper](https://github.com/MatthiasZepper)
 - [Maxime Garcia](https://github.com/maxulysse)
+- [Pieter Moris](https://github.com/pmoris)
 - [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 #1351](https://github.com/nf-core/rnaseq/pull/1351) - Adding Kraken2/Bracken on unaligned reads as an additional quality control step to detect sample contamination
+- [PR #1180](https://github.com/nf-core/rnaseq/pull/1180) - Bump pipeline version to 3.15.0dev
 - [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
@@ -75,7 +113,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1272](https://github.com/nf-core/rnaseq/pull/1272) - Simple pipeline level nf-tests
 - [PR #1274](https://github.com/nf-core/rnaseq/pull/1274) - Update bam_markduplicates_picard subworkflow
 - [PR #1278](https://github.com/nf-core/rnaseq/pull/1278) - Delocalise pseudo quant workflow
-- [PR #1279](https://github.com/nf-core/rnaseq/pull/1279) - Add psueudoaligner pipeline level tests to test suite
+- [PR #1279](https://github.com/nf-core/rnaseq/pull/1279) - Add pseudoaligner pipeline level tests to test suite
 - [PR #1280](https://github.com/nf-core/rnaseq/pull/1280) - Reorganise pipeline level tests into flat directory structure
 - [PR #1282](https://github.com/nf-core/rnaseq/pull/1282) - Fix CHANGELOG error
 - [PR #1283](https://github.com/nf-core/rnaseq/pull/1283) - Add output files to nf-test snapshot
@@ -103,13 +141,29 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1330](https://github.com/nf-core/rnaseq/pull/1330) - Update all nf-core/modules and subworkflows
 - [PR #1331](https://github.com/nf-core/rnaseq/pull/1331) - Adding stubs for local modules
 - [PR #1334](https://github.com/nf-core/rnaseq/pull/1334) - Update all nf-core/modules and subworkflows with stubs
-- [PR #1336](https://github.com/nf-core/rnaseq/pull/1334) - Use nf-core/setup-nf-test to install nf-test from cache during CI/CD
+- [PR #1335](https://github.com/nf-core/rnaseq/pull/1335) - Adding stubs at all levels
+- [PR #1336](https://github.com/nf-core/rnaseq/pull/1336) - Use nf-core/setup-nf-test to install nf-test from cache during CI/CD
 - [PR #1340](https://github.com/nf-core/rnaseq/pull/1340) - Remove out-of-date Azure specific guidance
 - [PR #1341](https://github.com/nf-core/rnaseq/pull/1341) - Add rename in the MultiQC report for samples without techreps
 - [PR #1342](https://github.com/nf-core/rnaseq/pull/1342) - Factor out preprocessing
 - [PR #1345](https://github.com/nf-core/rnaseq/pull/1345) - Fix preprocessing call
 - [PR #1350](https://github.com/nf-core/rnaseq/pull/1350) - Reduce resource usage for sort process in bedtools/genomecov
+- [PR #1352](https://github.com/nf-core/rnaseq/pull/1352) - Assorted fixes to MultiQC usage
 - [PR #1353](https://github.com/nf-core/rnaseq/pull/1353) - Correct conditional for salmon indexing in preprocessing workflow
+- [PR #1355](https://github.com/nf-core/rnaseq/pull/1355) - Make all curves on subway map better looking, and all lines now have the same width
+- [PR #1357](https://github.com/nf-core/rnaseq/pull/1357) - Fix anchor issue in multiqc
+- [PR #1358](https://github.com/nf-core/rnaseq/pull/1358) - Update test profiles to restore a static URI for megatests
+- [PR #1359](https://github.com/nf-core/rnaseq/pull/1359) - Update MultiQC and revert unnecessary workaround
+- [PR #1360](https://github.com/nf-core/rnaseq/pull/1360) - More complete snapshots for pipeline level tests
+- [PR #1361](https://github.com/nf-core/rnaseq/pull/1361) - Animate subway map
+- [PR #1362](https://github.com/nf-core/rnaseq/pull/1362) - Move multiqc module prefix for nf-test to module
+- [PR #1363](https://github.com/nf-core/rnaseq/pull/1363) - Minor updates of nf-core modules and subworkflows
+- [PR #1363](https://github.com/nf-core/rnaseq/pull/1363) - Update dupradar script
+- [PR #1366](https://github.com/nf-core/rnaseq/pull/1366) - Clarify docs on different tximport count files
+- [PR #1367](https://github.com/nf-core/rnaseq/pull/1367) - Clarify design formula and blind dispersion estimation
+- [PR #1370](https://github.com/nf-core/rnaseq/pull/1370) - Bump versions for 3.15.0
+- [PR #1371](https://github.com/nf-core/rnaseq/pull/1371) - Apply Maxime's CHANGELOG edits
+- [PR #1372](https://github.com/nf-core/rnaseq/pull/1372) - Bump tximeta/tximport for gene table row names fix
 
 ### Parameters
 
@@ -135,6 +189,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 | `samtools`                          | 1.17        | 1.20        |
 | `sortmerna`                         | 4.3.4       | 4.3.6       |
 | `umi_tools`                         | 1.14        | 1.15        |
+| `untar`                             | 1.3         | 1.34        |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present.
 >