Bump GTDB release version, better changelog

CHANGELOG.md

@@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- [#664](https://github.com/nf-core/mag/pull/664) - Update GTDBTk to latest version, with updated column names, update GTDB to release 220 (by @dialvarezs)
+
 ### `Fixed`
 
 ### `Dependencies`

conf/test_full.config

@@ -22,7 +22,7 @@ params {
     //centrifuge_db = "s3://ngi-igenomes/test-data/mag/p_compressed+h+v.tar.gz"
     kraken2_db    = "s3://ngi-igenomes/test-data/mag/minikraken_8GB_202003.tgz"
     cat_db        = "s3://ngi-igenomes/test-data/mag/CAT_prepare_20210107.tar.gz"
-    // gtdb_db       = "s3://ngi-igenomes/test-data/mag/gtdbtk_r214_data.tar.gz"
+    // gtdb_db       = "s3://ngi-igenomes/test-data/mag/gtdbtk_r214_data.tar.gz" ## This should be updated to release 220, once we get GTDB-Tk working again
     skip_gtdbtk   = true
 
     // TODO TEMPORARY: deactivate SPAdes due to incompatibility of container with fusion file system

nextflow.config

@@ -87,7 +87,7 @@ params {
     cat_official_taxonomy                = false
     save_cat_db                          = false
     skip_gtdbtk                          = false
-    gtdb_db                              = "https://data.ace.uq.edu.au/public/gtdb/data/releases/release214/214.1/auxillary_files/gtdbtk_r214_data.tar.gz"
+    gtdb_db                              = "https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r220_data.tar.gz"
     gtdb_mash                            = null
     gtdbtk_min_completeness              = 50.0
     gtdbtk_max_contamination             = 10.0

nextflow_schema.json

@@ -537,7 +537,7 @@
                 "gtdb_db": {
                     "type": "string",
                     "description": "Specify the location of a GTDBTK database. Can be either an uncompressed directory or a `.tar.gz` archive. If not specified will be downloaded for you when GTDBTK or binning QC is not skipped.",
-                    "default": "https://data.ace.uq.edu.au/public/gtdb/data/releases/release214/214.1/auxillary_files/gtdbtk_r214_data.tar.gz"
+                    "default": "https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r220_data.tar.gz"
                 },
                 "gtdb_mash": {
                     "type": "string",