docs: Update CHANGELOG and ARETE version

- Updates the changelog to reflect the changes ever since I started
  working on ARETE.
- Makes a new release

CHANGELOG.md

@@ -3,55 +3,108 @@
 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).
 
+## v2.0 dev - April 5, 2023
+
+### `Added`
+
+- Adds stubs to every process (2a990d48d1d024)
+- Adds assembly as a subworkflow (9e6d2679242)
+- Adds dbcache (50193b35)
+- Updates documentation
+  - README, ROADMAP, CITATIONS, docs/usage.md, docs/output.md
+- Adds test data (c57297ad922)
+
+- Reorganizes output directories by subworkflow (ff53e97129effb)
+- Adds option to skip Kraken2 (192ab2918997bb0d35d2195b8d3da)
+- **Adds unit tests to ARETE** (6a10be029268eb2f1d526913a8022a)
+- **Adds CI** (49eb2929f287643446c5eb073670435e45a559a9)
+- Adds initialization script to the workflow (300f52429ee9cee5e056)
+- **Make FastTree the default under the Phylo subwf** (b3a3ffa0e64367)
+- Adds light parameter to the workflow (b3a3ffa0e64367)
+- Concatenate and filter alignment results (8e738ef237bcc80b6d9)
+- **Adds PopPUNK** (d4ea29eaaad54905a81ca5a0c31a699c9ff89b2)
+- Updates and improves Bakta, making it the default(3cb354c9c6e20346e6a844e9a0c55060fb8dff)
+- Adds DIAMOND alignment against ICEberg2 (ed548cb8ac8bf44d68b)
+- **Adds IslandPath** (0c2ba57999f4952e1eb1db3b3107a4ccbdc5ad86)
+- **Adds VIBRANT** (f0b1f99a2c7ded75e6684e8775e052ca2ec6e140)
+- **Adds Integron Finder** (00735d15aa5d6fef67793fd32152ea91cfa65c2a)
+- **Adds Genome subsampling using PopPUNK distances** (af41029c9ce6d2308f3)
+
+### `Fixed`
+
+- Makes assembly and assemblyqc entries available (4fd48439be9)
+- Change databases to value channels so they can be recycled (1285c0582b5f78)
+- Adds missing params to config and schema (a2c2ea7d216b15f3652)
+- Integrate phylo subworkflow to the main pipeline (069400dde1d098fe)
+
+### `Deprecated`
+
+- Removed roary (786c69c223261846)
+- Removed orthofinder (8ce706a7a040d0)
+
 ## v.1.2.1 dev - March 18, 2022
 
-### `Added` 
+### `Added`
+
 - Add CheckM nf-core module
 - Add `assembly_qc` workflow; runs QC software on existing assemblies
 
 ### `Fixed`
+
 - Fixed MultiQC not finding QUAST report (again)
+
 ## v1.2.0 dev - January 19,2022
+
 Major refactoring to align with Nextflow DSL2 syntax.
+
 ### `Added`
+
 - Add SNPsites module
 - Add Diamond nf-core module
 - Add IQTree nf-core module
 
 ### `Fixed`
+
 - Fixed broken `assembly` workflow entry
 - Update most nf-core modules
 - Local software modules are now found in scripts rather than directories, as per nf-core v.2.0+ convention
 - Update directory structures, manifest files, Groovy files to nf-core v.2.0+ versions
 - Update default `max_retries` in config file to 2 (from 1)
 
 ### `Dependencies`
+
 - Bump nf-core to version 2.0+. (Note: nf-core is not required to run the pipeline, but module updates, linting etc require it)
 
 ### `Deprecated`
+
 - Local diamond module
 - Local IQTree module
 - Pathracer module currently not used. May be added back later
 
 ## v1.1dev - November 3, 2021
+
 Update of tools used with some debugging.
 
 ### `Added`
+
 - Add Roary for core genome alignment
 - Add Diamond functions for BLASTing VFDB, BacMet
 - Add 'annotation only' workflow
 - Add 'assembly only' workflow
 
 ### `Fixed`
+
 - Fixed MobSuite container
 - Fixed IQTree to work with Roary instead of Snippy
 - Fixed MultiQC to properly display reports from QUAST, Prokka
 - Update singularity containers where relevant
 
 ### `Dependencies`
+
 - No changes in dependencies
 
 ### `Deprecated`
+
 - Snippy module
 - Abricate module
 - CRISPR/CasFinder module

nextflow.config

@@ -174,7 +174,7 @@ manifest {
     description     = 'AMR/VF LGT-focused bacterial genomics workflow'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.04.0'
-    version         = '1.2dev'
+    version = '2.0dev'
 }
 
 // Function to ensure that resource requirements don't go beyond