Apply suggestions from code review

bin/taxref_reformat_qiime_greengenes2022.sh

@@ -1,9 +1,5 @@
 #!/bin/sh
 
 # Decompress files.
-gzip -c -d 2022.10.seqs.fna.gz > 2022.10.seqs.fna
-gzip -c -d 2022.10.taxonomy.md5.tsv.gz > 2022.10.taxonomy.md5.tsv
-
-# Select and rename files
-mv *.fna greengenes2022.fna
-mv *.tsv greengenes2022.tax
+gzip -c -d *.seqs.fna.gz > greengenes2.fna
+gzip -c -d *.taxonomy.md5.tsv.gz > greengenes2.tax

conf/ref_databases.config

@@ -330,7 +330,13 @@ params {
             citation = "McDonald, D., Price, M., Goodrich, J. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6, 610–618 (2012). https://doi.org/10.1038/ismej.2011.139"
             fmtscript = "taxref_reformat_qiime_greengenes85.sh"
         }
-        'greengenes2022' {
+        'greengenes2' {
+            title = "Greengenes2 16S - Version 2022.10"
+            file = [ "http://ftp.microbio.me/greengenes_release/2022.10/2022.10.seqs.fna.gz", "http://ftp.microbio.me/greengenes_release/2022.10/2022.10.taxonomy.md5.tsv.gz" ]
+            citation = "McDonald, D., Jiang, Y., Balaban, M. et al. Greengenes2 unifies microbial data in a single reference tree. Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01845-1"
+            fmtscript = "taxref_reformat_qiime_greengenes2022.sh"
+        }
+        'greengenes2=2022.10' {
             title = "Greengenes2 16S - Version 2022.10"
             file = [ "http://ftp.microbio.me/greengenes_release/2022.10/2022.10.seqs.fna.gz", "http://ftp.microbio.me/greengenes_release/2022.10/2022.10.taxonomy.md5.tsv.gz" ]
             citation = "McDonald, D., Jiang, Y., Balaban, M. et al. Greengenes2 unifies microbial data in a single reference tree. Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01845-1"

nextflow_schema.json

@@ -443,7 +443,8 @@
                         "unite-alleuk=8.2",
                         "unite-alleuk",
                         "greengenes85",
-                        "greengenes2022"
+                        "greengenes2",
+                        "greengenes2=2022.10"
                     ]
                 },
                 "qiime_ref_tax_custom": {