## What's Changed * Use singularity containers for PINTS by @edmundmiller in https://github.com/nf-core/nascent/pull/137 * Pass references as inputs by @edmundmiller in https://github.com/nf-core/nascent/pull/139 * Add HISAT2 by @edmundmiller in https://github.com/nf-core/nascent/pull/140 * build: Fix modules.json and bump subworkflows by @edmundmiller in https://github.com/nf-core/nascent/pull/141 * Add STAR aligner by @edmundmiller in https://github.com/nf-core/nascent/pull/142 * Update Modules by @edmundmiller in https://github.com/nf-core/nascent/pull/147 * Add citations to MultiQC by @edmundmiller in https://github.com/nf-core/nascent/pull/149 * Fix HOMER inputs by @edmundmiller in https://github.com/nf-core/nascent/pull/151 * Refactor tests by @edmundmiller in https://github.com/nf-core/nascent/pull/152 * Update HOMER docs by @edmundmiller in https://github.com/nf-core/nascent/pull/154 * Use BAM_RSEQC subworkflow by @edmundmiller in https://github.com/nf-core/nascent/pull/155 * Use official nf-test CI by @edmundmiller in https://github.com/nf-core/nascent/pull/157 * Cleanup output by @edmundmiller in https://github.com/nf-core/nascent/pull/156 * Fix GFFREAD bug by @edmundmiller in https://github.com/nf-core/nascent/pull/162 * style: Make version snapshots pretty by @edmundmiller in https://github.com/nf-core/nascent/pull/163 * Dynamic BWA MEM index memory by @edmundmiller in https://github.com/nf-core/nascent/pull/166 * Fix "Access to undefined parameter `forwardStranded`" warnings by @edmundmiller in https://github.com/nf-core/nascent/pull/170 * Clean up MultiQC and tests by @edmundmiller in https://github.com/nf-core/nascent/pull/171 * groHMM overhaul by @edmundmiller in https://github.com/nf-core/nascent/pull/165 * PINTS scatter gather by @edmundmiller in https://github.com/nf-core/nascent/pull/174 * Add HOMER uniqmap by @edmundmiller in https://github.com/nf-core/nascent/pull/175 * Clean groHMM publishing and remove `each` inputs by @edmundmiller in https://github.com/nf-core/nascent/pull/178 * chore: Remove old template by @edmundmiller in https://github.com/nf-core/nascent/pull/179 * Adopt nft-utils by @edmundmiller in https://github.com/nf-core/nascent/pull/182 * test(#57): Add uniqmap test by @edmundmiller in https://github.com/nf-core/nascent/pull/177 * chore: Fix config selectors by @edmundmiller in https://github.com/nf-core/nascent/pull/173 * Run lsp formatting by @edmundmiller in https://github.com/nf-core/nascent/pull/180 **Full Changelog**: https://github.com/nf-core/nascent/compare/2.2.0...2.3.0

### Added - [1494fff](https://github.com/nf-core/nascent/commit/1494fff2ecd8b498e19d7d0fa3f7ee0f71088ab4) - Update pipeline template to [nf-core/tools 2.12](https://github.com/nf-core/tools/releases/tag/2.12) - [ec24cfb](https://github.com/nf-core/nascent/commit/ec24cfb2646904bcc78379a071b50b53a855b9a9) - Update pipeline template to [nf-core/tools 2.11.1](https://github.com/nf-core/tools/releases/tag/2.11.1) - [15b8ff3](https://github.com/nf-core/nascent/commit/15b8ff31cd43ec2e330ce7958bd6d7d65529b4d3) - Update pipeline template to [nf-core/tools 2.11](https://github.com/nf-core/tools/releases/tag/2.11) - [9712163](https://github.com/nf-core/nascent/commit/97121638eb77e175b912ff45a669426e532c5d7f) - Update pipeline template to [nf-core/tools 2.10](https://github.com/nf-core/tools/releases/tag/2.10) - [[#130](https://github.com/nf-core/nascent/pull/130)] - AWS Mega Tests - [[#132](https://github.com/nf-core/nascent/pull/132)] - Add Bowtie 2 as an aligner option ### Changed - [[#117](https://github.com/nf-core/nascent/pull/117)] - Use fromSamplesheet - Updating naming scheme to use things from the Dune universe

### Fixed - [[#109](https://github.com/nf-core/nascent/pull/109)] - Fixed bug where using AWS igenomes or passing a pre-made index fails because of an update to the module expects them to have a metamap. Generation was still working. (@MathewBerg9) **Full Changelog**: https://github.com/nf-core/nascent/compare/2.1.0...2.1.1