Version bump

CHANGELOG.md

@@ -3,21 +3,38 @@
 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).
 
-## v2.0.0 - [date]
+## [[2.0.0](https://github.com/sanger-tol/insdcdownload/releases/tag/2.0.0)] – Light elf – [2024-05-24]
 
-### `Fixed`
+This version supports the new FTP structure of Ensembl
+
+### Enhancements & fixes
 
 - The sample-sheet column `species_dir` is replaced with the `outdir` column which
   represents where the assembly and repeats are downloaded (in immediate sub-directories)
 - Relative paths in the sample-sheet are now evaluated from the `--outdir` parameter
 - Memory usage rules for `samtools dict`
 - Appropriate use of `tabix`'s TBI and CSI indexing, depending on the sequence lengths
+- `--outdir` is a _mandatory_ parameter
 
-### `Added`
+### Parameters
 
-- `--outdir` is a _mandatory_ parameter
+_In the samplesheet_
+
+| Old parameter | New parameter     |
+| ------------- | ----------------- |
+| species_dir   | outdir            |
+
+> **NB:** Parameter has been **updated** if both old and new parameter information is present. </br> **NB:** Parameter has been **added** if just the new parameter information is present. </br> **NB:** Parameter has been **removed** if new parameter information isn't present.
+
+### Software dependencies
+
+Note, since the pipeline is using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference. Only `Docker` or `Singularity` containers are supported, `conda` is not supported.
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| multiqc    | 1.13        | 1.14        |
 
-## v1.1.0 - [2022-10-07]
+## [[1.1.0](https://github.com/sanger-tol/insdcdownload/releases/tag/1.1.0)] – Deciduous ent – [2022-10-07]
 
 Minor update that fixes a few bugs
 
@@ -30,7 +47,7 @@ Minor update that fixes a few bugs
 
 - New `species_dir` column to indicate where to download the files to
 
-## v1.0.0 - [2022-08-12]
+## [[1.0.0](https://github.com/sanger-tol/insdcdownload/releases/tag/1.0.0)] – Flaming balrog – [2022-08-12]
 
 Initial release of sanger-tol/insdcdownload, created with the [nf-core](https://nf-co.re/) template.
 

CITATION.cff

@@ -2,7 +2,7 @@
 # Visit https://bit.ly/cffinit to generate yours today!
 
 cff-version: 1.2.0
-title: sanger-tol/insdcdownload v1.1.0 - Deciduous ent
+title: sanger-tol/insdcdownload
 message: >-
     If you use this software, please cite it using the
     metadata from this file.
@@ -22,5 +22,5 @@ identifiers:
 repository-code: "https://github.com/sanger-tol/insdcdownload"
 license: MIT
 commit: TODO
-version: 1.1.0
+version: 2.0.0
 date-released: "2022-10-07"

nextflow.config

@@ -204,7 +204,7 @@ manifest {
     description     = """Pipeline that downloads assemblies from INSDC into a Tree of Life directory structure"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.2dev'
+    version         = '2.0.0'
     doi             = '10.5281/zenodo.6983932'
 }