bump Qiime2 to 2023.9

config/config.yaml

@@ -1,11 +1,11 @@
 # Qiime2 version number
-q2v: "2023.7"
+q2v: "2023.9"
 # Qiime2 conda environment
 # Get full file from from https://github.com/qiime2/environment-files
 # Or specify name of already installed Qiime2 environment
-q2env: "qiime2-2023.7"
+q2env: "qiime2-amplicon-2023.9"
 # Or load a pre-installed module
-q2mod: "qiime2/2023.7"
+q2mod: "qiime2/2023.9"
 
 # UNITE Major version listed in file names
 version: "ver9"

release_notes_newest.md

@@ -1,30 +1,27 @@
 ⚠️ This is a public demo, and has not been validated. I am not affiliated with the UNITE team.
 
-This is a classifier for [Unite v9.0](https://unite.ut.ee/repository.php) Version 18.07.2023 trained for use with [Qiime2 2023.7](https://docs.qiime2.org/2023.7/install/).
-These can be used with `q2-feature-classifier` like those found on the [Data resources page](https://docs.qiime2.org/2023.7/data-resources/).
+This is a classifier for [Unite v9.0](https://unite.ut.ee/repository.php) Version 18.07.2023 trained for use with [Qiime2 2023.9](https://docs.qiime2.org/2023.9/install/).
+These can be used with `q2-feature-classifier` like those found on the [Data resources page](https://docs.qiime2.org/2023.9/data-resources/).
 
 UNITE is licensed under CC BY-SA 4.0. If you use it, cite it! 🤝
 
->Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2022): UNITE QIIME release for Fungi. Version 18.07.2023. UNITE Community **\<DOI GOES HERE>**
+>Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2023): UNITE QIIME release for Fungi. Version 18.07.2023. UNITE Community **\<DOI GOES HERE>**
 >
 > DOIs for specific releases are listed here: https://unite.ut.ee/repository.php
 
 ---
 
 Changes:
 
-- Update Qiime2 to version 2023.7
-- Internal changes:
-  - Add basic benchmarks
-  - Change default cluster settings
-  - Import using new MixedCaseDNAFASTAFormat (thanks @mikerobeson!)
+- Update Qiime2 to version 2023.9
+- This should work with all three distributions: amplicon, shotgun, and tidy. If not, please [open an issue! ✅](https://github.com/colinbrislawn/unite-train/issues)
 
 ---
 
 There are two levels of classification provided here:
 
-- "99", which is 99% identity between taxa
-- "dynamic", which uses 97% to 99% identity between taxa, as individually recommended by experts in the field.
+- "99", in which the database is clustered at 99% identity between taxa
+- "dynamic", which uses 97% to 99% identity between taxa, as individually recommended by experts in the field
 
 There are two taxa scopes:
 
@@ -33,9 +30,9 @@ There are two taxa scopes:
 
 There two versions, with and without an "s":
 
-- "" Includes singletons set as RefS (in dynamic files).
+- "" Includes singletons set as RefS (in dynamic files)
 - "s" Includes global and 97% singletons.
-  (I'm not sure what that means.)
+  (I'm not sure what that means)
 
 ---
 

release_to_GitHub.md

@@ -21,7 +21,7 @@ export TMPDIR="/tmp/qiime2tmp/"
 module load qiime2
 
 time qiime feature-classifier classify-sklearn \
-  --i-classifier unite_ver9_dynamic_25.07.2023-Q2-2023.7.qza \
+  --i-classifier unite_ver9_dynamic_25.07.2023-Q2-2023.9.qza \
   --i-reads ../benchmarks/dada2-single-end-rep-seqs.qza \
   --o-classification test-tax.qza
 
@@ -38,14 +38,14 @@ rm -rf test-tax*
 ## Create a new tag and release:
 
 ```bash
-newtag="v9.0-v25.07.2023-qiime2-2023.7"
+newtag="v9.0-v25.07.2023-qiime2-2023.9"
 
 gh release create ${newtag} \
   --draft \
   --latest \
   -F release_notes_newest.md \
   --prerelease  \
-  --title "UNITE v9.0 v25.07.2023 for qiime2-2023.7"
+  --title "UNITE v9.0 v25.07.2023 for qiime2-2023.9"
 ```
 
 ## Push files to this new release: