From e5e8f370422fcce7c48f3697d85cf94c1cdc5fac Mon Sep 17 00:00:00 2001
From: Daniel Lundin <erik.rikard.daniel@gmail.com>
Date: Tue, 23 Jul 2024 19:09:03 +0200
Subject: [PATCH 01/15] Work on SINTAX/UNITE dbs

---
 ...tax.sh => taxref_reformat_sintax_fasta.sh} |  1 -
 bin/taxref_reformat_sintax_tar.sh             | 13 ++++
 conf/ref_databases.config                     | 74 ++++++++++++-------
 nextflow_schema.json                          | 16 ++--
 4 files changed, 70 insertions(+), 34 deletions(-)
 rename bin/{taxref_reformat_sintax.sh => taxref_reformat_sintax_fasta.sh} (99%)
 create mode 100755 bin/taxref_reformat_sintax_tar.sh

diff --git a/bin/taxref_reformat_sintax.sh b/bin/taxref_reformat_sintax_fasta.sh
similarity index 99%
rename from bin/taxref_reformat_sintax.sh
rename to bin/taxref_reformat_sintax_fasta.sh
index b076d0af0..30e63fca7 100755
--- a/bin/taxref_reformat_sintax.sh
+++ b/bin/taxref_reformat_sintax_fasta.sh
@@ -5,4 +5,3 @@
 # Just rename the preformatted file
 # Assumes only one (gzipped) file
 mv * sintaxdb.fa.gz
-
diff --git a/bin/taxref_reformat_sintax_tar.sh b/bin/taxref_reformat_sintax_tar.sh
new file mode 100755
index 000000000..2d999cf63
--- /dev/null
+++ b/bin/taxref_reformat_sintax_tar.sh
@@ -0,0 +1,13 @@
+#!/bin/sh
+
+# Handles preformatted database files suitable for sintax
+
+# Just rename the preformatted file
+# Assumes only one (gzipped) file
+
+# Extract the fasta file without _dev in its name
+tar xzf *.tgz $(tar tfz *.tgz | grep -v '_dev')
+
+# Change the name and gzip
+mv *.fasta sintaxdb.fa
+gzip sintaxdb.fa
diff --git a/conf/ref_databases.config b/conf/ref_databases.config
index c2db0ed21..2a95bc75a 100644
--- a/conf/ref_databases.config
+++ b/conf/ref_databases.config
@@ -130,11 +130,19 @@ params {
             dbversion = "RDP 18/11.5 (https://zenodo.org/record/4310151/)"
         }
         'sbdi-gtdb' {
-            title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R08-RS214-1"
-            file = [ "https://figshare.scilifelab.se/ndownloader/files/45818841", "https://figshare.scilifelab.se/ndownloader/files/45818850" ]
+            title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R09-RS220-1"
+            file = [ "https://figshare.scilifelab.se/ndownloader/files/47244061", "https://figshare.scilifelab.se/ndownloader/files/47244076" ]
             citation = "Lundin D, Andersson A. SBDI Sativa curated 16S GTDB database. FigShare. doi: 10.17044/scilifelab.14869077.v6"
             fmtscript = "taxref_reformat_sbdi-gtdb.sh"
-            dbversion = "SBDI-GTDB-R08-RS214-1 (https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/6)"
+            dbversion = "SBDI-GTDB-R09-RS220-1 (https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/7)"
+            taxlevels = "Domain,Kingdom,Phylum,Class,Order,Family,Genus,Species"
+        }
+        'sbdi-gtdb=R09-RS220-1' {
+            title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R09-RS220-1"
+            file = [ "https://figshare.scilifelab.se/ndownloader/files/47244061", "https://figshare.scilifelab.se/ndownloader/files/47244076" ]
+            citation = "Lundin D, Andersson A. SBDI Sativa curated 16S GTDB database. FigShare. doi: 10.17044/scilifelab.14869077.v6"
+            fmtscript = "taxref_reformat_sbdi-gtdb.sh"
+            dbversion = "SBDI-GTDB-R09-RS220-1 (https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/7)"
             taxlevels = "Domain,Kingdom,Phylum,Class,Order,Family,Genus,Species"
         }
         'sbdi-gtdb=R08-RS214-1' {
@@ -192,7 +200,7 @@ params {
         }
         'unite-fungi' {
             title = "UNITE general FASTA release for Fungi - Version 9.0"
-            file = [ "https://files.plutof.ut.ee/public/orig/1E/25/1E25CA4CC30A31C2E2B8CB2C89824C83D080A7F5A62E6263A0E95B37C6628067.tgz" ]
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/fa1038da-d18d-46b7-88a9-c21bcf38c43d.tgz" ]
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2022): UNITE general FASTA release for Fungi. Version 16.10.2022. UNITE Community. https://doi.org/10.15156/BIO/2483911"
             fmtscript = "taxref_reformat_unite.sh"
             dbversion = "UNITE-fungi v9.0 (https://doi.org/10.15156/BIO/2483911)"
@@ -200,7 +208,7 @@ params {
         }
         'unite-fungi=9.0' {
             title = "UNITE general FASTA release for Fungi - Version 9.0"
-            file = [ "https://files.plutof.ut.ee/public/orig/1E/25/1E25CA4CC30A31C2E2B8CB2C89824C83D080A7F5A62E6263A0E95B37C6628067.tgz" ]
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/fa1038da-d18d-46b7-88a9-c21bcf38c43d.tgz" ]
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2022): UNITE general FASTA release for Fungi. Version 16.10.2022. UNITE Community. https://doi.org/10.15156/BIO/2483911"
             fmtscript = "taxref_reformat_unite.sh"
             dbversion = "UNITE-fungi v9.0 (https://doi.org/10.15156/BIO/2483911)"
@@ -356,7 +364,7 @@ params {
             title = "COIDB - CO1 Taxonomy Database - Release 221216"
             file = [ "https://figshare.scilifelab.se/ndownloader/files/38787078" ]
             citation = "Sundh J, Manoharan L, Iwaszkiewicz-Eggebrecht E, Miraldo A, Andersson A, Ronquist F. COI reference sequences from BOLD DB. doi: https://doi.org/10.17044/scilifelab.20514192.v2"
-            fmtscript = "taxref_reformat_sintax.sh"
+            fmtscript = "taxref_reformat_sintax_fasta.sh"
             dbversion = "COIDB 221216 (https://doi.org/10.17044/scilifelab.20514192.v2)"
             taxlevels = "Kingdom,Phylum,Class,Order,Family,Genus,Species,BOLD_bin"
         }
@@ -364,64 +372,78 @@ params {
             title = "COIDB - CO1 Taxonomy Database - Release 221216"
             file = [ "https://figshare.scilifelab.se/ndownloader/files/38787078" ]
             citation = "Sundh J, Manoharan L, Iwaszkiewicz-Eggebrecht E, Miraldo A, Andersson A, Ronquist F. COI reference sequences from BOLD DB. doi: https://doi.org/10.17044/scilifelab.20514192.v2"
-            fmtscript = "taxref_reformat_sintax.sh"
+            fmtscript = "taxref_reformat_sintax_fasta.sh"
             dbversion = "COIDB 221216 (https://doi.org/10.17044/scilifelab.20514192.v2)"
             taxlevels = "Kingdom,Phylum,Class,Order,Family,Genus,Species,BOLD_bin"
         }
         'unite-fungi' {
-            title = "UNITE USEARCH/UTAX release for Fungi - Version 9.0"
-            file = [ "https://files.plutof.ut.ee/public/orig/19/1B/191B0D889A6B7B05DF4C103B118ABB3E0CF8EDBEA5B3E3FAB3EAFE3B72D7F3C8.gz" ]
-            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2022): UNITE USEARCH/UTAX release for Fungi. Version 16.10.2022. UNITE Community. https://doi.org/10.15156/BIO/2483923"
-            fmtscript = "taxref_reformat_sintax.sh"
-            dbversion = "UNITE-fungi v9.0 (https://doi.org/10.15156/BIO/2483923)"
+            title = "UNITE USEARCH/UTAX release for Fungi - Version 10.0"
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/d18aa648-3f4c-4f46-84d4-c8c5d48439ba.tgz" ]
+            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2024): UNITE USEARCH/UTAX release for Fungi. UNITE Community. 10.15156/BIO/2959340"
+            fmtscript = "taxref_reformat_sintax_tar.sh"
+            dbversion = "UNITE-fungi v10.0 (https://doi.plutof.ut.ee/doi/10.15156/BIO/2959340)"
+        }
+        'unite-fungi=10.0' {
+            title = "UNITE USEARCH/UTAX release for Fungi - Version 10.0"
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/d18aa648-3f4c-4f46-84d4-c8c5d48439ba.tgz" ]
+            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2024): UNITE USEARCH/UTAX release for Fungi. UNITE Community. 10.15156/BIO/2959340"
+            fmtscript = "taxref_reformat_sintax_tar.sh"
+            dbversion = "UNITE-fungi v10.0 (https://doi.plutof.ut.ee/doi/10.15156/BIO/2959340)"
         }
         'unite-fungi=9.0' {
             title = "UNITE USEARCH/UTAX release for Fungi - Version 9.0"
-            file = [ "https://files.plutof.ut.ee/public/orig/19/1B/191B0D889A6B7B05DF4C103B118ABB3E0CF8EDBEA5B3E3FAB3EAFE3B72D7F3C8.gz" ]
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/fa1038da-d18d-46b7-88a9-c21bcf38c43d.tgz" ]
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2022): UNITE USEARCH/UTAX release for Fungi. Version 16.10.2022. UNITE Community. https://doi.org/10.15156/BIO/2483923"
-            fmtscript = "taxref_reformat_sintax.sh"
+            fmtscript = "taxref_reformat_sintax_tar.sh"
             dbversion = "UNITE-fungi v9.0 (https://doi.org/10.15156/BIO/2483923)"
         }
         'unite-fungi=8.3' {
             title = "UNITE USEARCH/UTAX release for Fungi - Version 8.3"
-            file = [ "https://files.plutof.ut.ee/public/orig/82/CB/82CB44BBAAA7D3AEAC297B5689BDA2963E8D0666E01FE0B54096147AFAF85263.gz" ]
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/5f5085d1-ff89-4e9d-9c85-12165dcbf880.gz" ]
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2021): UNITE USEARCH/UTAX release for Fungi. UNITE Community. 10.15156/BIO/1280276"
-            fmtscript = "taxref_reformat_sintax.sh"
+            fmtscript = "taxref_reformat_sintax_fasta.sh"
             dbversion = "UNITE-fungi v8.3 (https://dx.doi.org/10.15156/BIO/1280276)"
         }
         'unite-fungi=8.2' {
             title = "UNITE USEARCH/UTAX release for Fungi - Version 8.2"
-            file = [ "https://files.plutof.ut.ee/public/orig/E8/83/E883EB19E3EA7B64C1F652521301239831FAFE0BFF015C9E2B4786DC0976C0FC.gz" ]
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/a6c4d680-c99a-4252-ba67-748271c7d7f4.gz" ]
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2020): UNITE USEARCH/UTAX release for Fungi. UNITE Community. 10.15156/BIO/786375"
-            fmtscript = "taxref_reformat_sintax.sh"
+            fmtscript = "taxref_reformat_sintax_fasta.sh"
             dbversion = "UNITE-fungi v8.2 (https://doi.org/10.15156/BIO/786375)"
         }
         'unite-alleuk' {
-            title = "UNITE USEARCH/UTAX release for eukaryotes - Version 9.0"
-            file = [ "https://files.plutof.ut.ee/public/orig/AB/8C/AB8C119FC82CF5AFAFCB93CA4FFFF2B42A03CF1275DE23F60B887392E8FDEA21.gz"]
-            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2022): UNITE USEARCH/UTAX release for eukaryotes. Version 16.10.2022. UNITE Community. https://doi.org/10.15156/BIO/2483924"
-            fmtscript = "taxref_reformat_sintax.sh"
-            dbversion = "UNITE-alleuk v9.0 (https://doi.org/10.15156/BIO/2483924)"
+            title = "UNITE USEARCH/UTAX release for eukaryotes - Version 10.0"
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/6f19ddb6-1ac0-4834-a74c-b639688878a4.gz" ]
+            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2024): UNITE USEARCH/UTAX release for eukaryotes. Version 04.04.2024. UNITE Community. https://doi.org/10.15156/BIO/2959341"
+            fmtscript = "taxref_reformat_sintax_fasta.sh"
+            dbversion = "UNITE-alleuk v10.0 (https://doi.org/10.15156/BIO/2959341)"
+        }
+        'unite-alleuk=10.0' {
+            title = "UNITE USEARCH/UTAX release for eukaryotes - Version 10.0"
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/6f19ddb6-1ac0-4834-a74c-b639688878a4.gz" ]
+            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2024): UNITE USEARCH/UTAX release for eukaryotes. Version 04.04.2024. UNITE Community. https://doi.org/10.15156/BIO/2959341"
+            fmtscript = "taxref_reformat_sintax_fasta.sh"
+            dbversion = "UNITE-alleuk v10.0 (https://doi.org/10.15156/BIO/2959341)"
         }
         'unite-alleuk=9.0' {
             title = "UNITE USEARCH/UTAX release for eukaryotes - Version 9.0"
             file = [ "https://files.plutof.ut.ee/public/orig/AB/8C/AB8C119FC82CF5AFAFCB93CA4FFFF2B42A03CF1275DE23F60B887392E8FDEA21.gz"]
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2022): UNITE USEARCH/UTAX release for eukaryotes. Version 16.10.2022. UNITE Community. https://doi.org/10.15156/BIO/2483924"
-            fmtscript = "taxref_reformat_sintax.sh"
+            fmtscript = "taxref_reformat_sintax_tar.sh"
             dbversion = "UNITE-alleuk v9.0 (https://doi.org/10.15156/BIO/2483924)"
         }
         'unite-alleuk=8.3' {
             title = "UNITE USEARCH/UTAX release for eukaryotes - Version 8.3"
             file = [ "https://files.plutof.ut.ee/public/orig/B9/35/B9351C91550A52713CB66DB7A1CEF35765310EBB23B6667AC93E714E9A9D020B.gz"]
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2021): UNITE USEARCH/UTAX release for eukaryotes. UNITE Community. 10.15156/BIO/1280317"
-            fmtscript = "taxref_reformat_sintax.sh"
+            fmtscript = "taxref_reformat_sintax_fasta.sh"
             dbversion = "UNITE-alleuk v8.3 (https://doi.org/10.15156/BIO/1280127)"
         }
         'unite-alleuk=8.2' {
             title = "UNITE USEARCH/UTAX release for eukaryotes - Version 8.2"
             file = [ "https://files.plutof.ut.ee/public/orig/7B/B5/7BB51166C988E448392B213A72D4604E2ABB494E20E19E4392F7819FEBFCD036.gz"]
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2020): UNITE USEARCH/UTAX release for eukaryotes. UNITE Community. 10.15156/BIO/786376"
-            fmtscript = "taxref_reformat_sintax.sh"
+            fmtscript = "taxref_reformat_sintax_fasta.sh"
             dbversion = "UNITE-alleuk v8.2 (https://dx.doi.org/10.15156/BIO/786376)"
         }
     }
diff --git a/nextflow_schema.json b/nextflow_schema.json
index ceaf9366b..c3917d985 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -380,13 +380,13 @@
                         "silva=132",
                         "silva=138",
                         "unite-alleuk",
-                        "unite-alleuk=8.2",
-                        "unite-alleuk=8.3",
                         "unite-alleuk=9.0",
+                        "unite-alleuk=8.3",
+                        "unite-alleuk=8.2",
                         "unite-fungi",
-                        "unite-fungi=8.2",
-                        "unite-fungi=8.3",
                         "unite-fungi=9.0",
+                        "unite-fungi=8.3",
+                        "unite-fungi=8.2",
                         "zehr-nifh",
                         "zehr-nifh=2.5.0"
                     ]
@@ -519,14 +519,16 @@
                     "enum": [
                         "coidb",
                         "coidb=221216",
+                        "unite-fungi",
+                        "unite-fungi=10.0",
                         "unite-fungi=9.0",
                         "unite-fungi=8.3",
                         "unite-fungi=8.2",
-                        "unite-fungi",
+                        "unite-alleuk",
+                        "unite-alleuk=10.0",
                         "unite-alleuk=9.0",
                         "unite-alleuk=8.3",
-                        "unite-alleuk=8.2",
-                        "unite-alleuk"
+                        "unite-alleuk=8.2"
                     ]
                 },
                 "addsh": {

From a6419cea11a2d91326d2ddd92ab25f247c008f78 Mon Sep 17 00:00:00 2001
From: Daniel Lundin <erik.rikard.daniel@gmail.com>
Date: Tue, 23 Jul 2024 19:59:01 +0200
Subject: [PATCH 02/15] SINTAX/UNITE fixed urls

---
 bin/taxref_reformat_sintax_tar.sh                      |  5 +++--
 conf/ref_databases.config                              | 10 +++++-----
 .../local/utils_nfcore_ampliseq_pipeline/main.nf       |  4 ++--
 3 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/bin/taxref_reformat_sintax_tar.sh b/bin/taxref_reformat_sintax_tar.sh
index 2d999cf63..8539084d9 100755
--- a/bin/taxref_reformat_sintax_tar.sh
+++ b/bin/taxref_reformat_sintax_tar.sh
@@ -6,8 +6,9 @@
 # Assumes only one (gzipped) file
 
 # Extract the fasta file without _dev in its name
-tar xzf *.tgz $(tar tfz *.tgz | grep -v '_dev')
+f=$(tar tfz *.tgz | grep fasta | grep -v '_dev')
+tar xzf *.tgz $f
 
 # Change the name and gzip
-mv *.fasta sintaxdb.fa
+mv $f sintaxdb.fa
 gzip sintaxdb.fa
diff --git a/conf/ref_databases.config b/conf/ref_databases.config
index 2a95bc75a..97ba3de08 100644
--- a/conf/ref_databases.config
+++ b/conf/ref_databases.config
@@ -427,21 +427,21 @@ params {
         }
         'unite-alleuk=9.0' {
             title = "UNITE USEARCH/UTAX release for eukaryotes - Version 9.0"
-            file = [ "https://files.plutof.ut.ee/public/orig/AB/8C/AB8C119FC82CF5AFAFCB93CA4FFFF2B42A03CF1275DE23F60B887392E8FDEA21.gz"]
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/00853437-b8b3-4d94-bcd8-7b942fcd8aa2.gz" ]
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2022): UNITE USEARCH/UTAX release for eukaryotes. Version 16.10.2022. UNITE Community. https://doi.org/10.15156/BIO/2483924"
-            fmtscript = "taxref_reformat_sintax_tar.sh"
+            fmtscript = "taxref_reformat_sintax_fasta.sh"
             dbversion = "UNITE-alleuk v9.0 (https://doi.org/10.15156/BIO/2483924)"
         }
         'unite-alleuk=8.3' {
             title = "UNITE USEARCH/UTAX release for eukaryotes - Version 8.3"
-            file = [ "https://files.plutof.ut.ee/public/orig/B9/35/B9351C91550A52713CB66DB7A1CEF35765310EBB23B6667AC93E714E9A9D020B.gz"]
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/6e72e839-acfc-4044-84b4-5152b74c1552.tgz" ]
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2021): UNITE USEARCH/UTAX release for eukaryotes. UNITE Community. 10.15156/BIO/1280317"
-            fmtscript = "taxref_reformat_sintax_fasta.sh"
+            fmtscript = "taxref_reformat_sintax_tar.sh"
             dbversion = "UNITE-alleuk v8.3 (https://doi.org/10.15156/BIO/1280127)"
         }
         'unite-alleuk=8.2' {
             title = "UNITE USEARCH/UTAX release for eukaryotes - Version 8.2"
-            file = [ "https://files.plutof.ut.ee/public/orig/7B/B5/7BB51166C988E448392B213A72D4604E2ABB494E20E19E4392F7819FEBFCD036.gz"]
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/fd6411cf-2c68-42e5-ae94-13ffb933a5c5.gz" ]
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2020): UNITE USEARCH/UTAX release for eukaryotes. UNITE Community. 10.15156/BIO/786376"
             fmtscript = "taxref_reformat_sintax_fasta.sh"
             dbversion = "UNITE-alleuk v8.2 (https://dx.doi.org/10.15156/BIO/786376)"
diff --git a/subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf
index 6a31f97f9..a1c190fcd 100644
--- a/subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf
@@ -245,8 +245,8 @@ def validateInputParameters() {
         "rdp","rdp=18",
         "sbdi-gtdb","sbdi-gtdb=R09-RS220-1","sbdi-gtdb=R08-RS214-1","sbdi-gtdb=R07-RS207-1",
         "silva","silva=138","silva=132",
-        "unite-fungi","unite-fungi=9.0","unite-fungi=8.3","unite-fungi=8.2",
-        "unite-alleuk","unite-alleuk=9.0","unite-alleuk=8.3","unite-alleuk=8.2"
+        "unite-fungi","unite-fungi=10.0","unite-fungi=9.0","unite-fungi=8.3","unite-fungi=8.2",
+        "unite-alleuk","unite-alleuk=10.0","unite-alleuk=9.0","unite-alleuk=8.3","unite-alleuk=8.2"
     ]
     if (params.sbdiexport){
         if (params.sintax_ref_taxonomy ) {

From be87d1b47625b0954a6e6ac47b1d0e161a25164d Mon Sep 17 00:00:00 2001
From: Daniel Lundin <erik.rikard.daniel@gmail.com>
Date: Tue, 23 Jul 2024 21:03:39 +0200
Subject: [PATCH 03/15] Updated DADA UNITE urls

---
 conf/ref_databases.config          | 38 +++++++++++------------
 conf/test_its_dada_taxonomy.config | 50 ++++++++++++++++++++++++++++++
 nextflow.config                    | 31 +++++++++---------
 3 files changed, 85 insertions(+), 34 deletions(-)
 create mode 100644 conf/test_its_dada_taxonomy.config

diff --git a/conf/ref_databases.config b/conf/ref_databases.config
index 97ba3de08..688d571c3 100644
--- a/conf/ref_databases.config
+++ b/conf/ref_databases.config
@@ -201,63 +201,63 @@ params {
         'unite-fungi' {
             title = "UNITE general FASTA release for Fungi - Version 9.0"
             file = [ "https://s3.hpc.ut.ee/plutof-public/original/fa1038da-d18d-46b7-88a9-c21bcf38c43d.tgz" ]
-            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2022): UNITE general FASTA release for Fungi. Version 16.10.2022. UNITE Community. https://doi.org/10.15156/BIO/2483911"
+            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2023): UNITE general FASTA release for Fungi. Version 18.07.2023. UNITE Community. https://doi.org/10.15156/BIO/2938067"
             fmtscript = "taxref_reformat_unite.sh"
-            dbversion = "UNITE-fungi v9.0 (https://doi.org/10.15156/BIO/2483911)"
+            dbversion = "UNITE-fungi v9.0 (https://doi.org/10.15156/BIO/2938067)"
             shfile = [ "https://figshare.scilifelab.se/ndownloader/files/40788767", "https://figshare.scilifelab.se/ndownloader/files/40788770"]
         }
         'unite-fungi=9.0' {
             title = "UNITE general FASTA release for Fungi - Version 9.0"
             file = [ "https://s3.hpc.ut.ee/plutof-public/original/fa1038da-d18d-46b7-88a9-c21bcf38c43d.tgz" ]
-            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2022): UNITE general FASTA release for Fungi. Version 16.10.2022. UNITE Community. https://doi.org/10.15156/BIO/2483911"
+            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2023): UNITE general FASTA release for Fungi. Version 18.07.2023. UNITE Community. https://doi.org/10.15156/BIO/2938067"
             fmtscript = "taxref_reformat_unite.sh"
-            dbversion = "UNITE-fungi v9.0 (https://doi.org/10.15156/BIO/2483911)"
+            dbversion = "UNITE-fungi v9.0 (https://doi.org/10.15156/BIO/2938067)"
             shfile = [ "https://figshare.scilifelab.se/ndownloader/files/40788767", "https://figshare.scilifelab.se/ndownloader/files/40788770"]
         }
         'unite-fungi=8.3' {
             title = "UNITE general FASTA release for Fungi - Version 8.3"
-            file = [ "https://files.plutof.ut.ee/public/orig/7B/23/7B235835FAF5C85D7B01E40FEF17F687914CB81A182554C5BD95E3168328E604.tgz" ]
-            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2021): UNITE general FASTA release for Fungi. UNITE Community. 10.15156/BIO/1280049"
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/a0d487ac-1339-4bea-a0e9-8627f87a2f88.tgz" ]
+            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2021): UNITE general FASTA release for Fungi. Version 10.05.2021. UNITE Community. https://doi.org/10.15156/BIO/1280049"
             fmtscript = "taxref_reformat_unite.sh"
             dbversion = "UNITE-fungi v8.3 (https://doi.org/10.15156/BIO/1280049)"
             shfile = [ "https://scilifelab.figshare.com/ndownloader/files/34497977", "https://scilifelab.figshare.com/ndownloader/files/34497980"]
         }
         'unite-fungi=8.2' {
             title = "UNITE general FASTA release for Fungi - Version 8.2"
-            file = [ "https://files.plutof.ut.ee/public/orig/E7/28/E728E2CAB797C90A01CD271118F574B8B7D0DAEAB7E81193EB89A2AC769A0896.gz" ]
-            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2020): UNITE general FASTA release for Fungi. UNITE Community. 10.15156/BIO/786368"
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/6fdb458a-9299-41dc-8774-5152b867d882.gz" ]
+            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2020): UNITE general FASTA release for Fungi. Version 04.02.2020. UNITE Community. https://doi.org/10.15156/BIO/786368"
             fmtscript = "taxref_reformat_unite.sh"
-            dbversion = "UNITE-fungi v8.2 (https://doi.org/10.15156/BIO/786368)"
+            dbversion = "UNITE-fungi v8.2 (https://doi.plutof.ut.ee/doi/10.15156/BIO/786368)"
             shfile = [ "https://scilifelab.figshare.com/ndownloader/files/34497971", "https://scilifelab.figshare.com/ndownloader/files/34497974"]
         }
         'unite-alleuk' {
             title = "UNITE general FASTA release for eukaryotes - Version 9.0"
-            file = [ "https://files.plutof.ut.ee/public/orig/F2/62/F262D942DEB8CAB3AEB9F313F67B04050E364B72E6707F99755DDCB271C45A48.tgz" ]
-            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2022): UNITE general FASTA release for eukaryotes. Version 16.10.2022. UNITE Community. https://doi.org/10.15156/BIO/2483913"
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/e318f5fd-1ef4-40fd-9e77-1b94d91b3858.tgz" ]
+            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2023): UNITE general FASTA release for eukaryotes. Version 18.07.2023. UNITE Community. https://doi.org/10.15156/BIO/2938069"
             fmtscript = "taxref_reformat_unite.sh"
-            dbversion = "UNITE-alleuk v9.0 (https://doi.org/10.15156/BIO/2483913)"
+            dbversion = "UNITE-alleuk v9.0 (https://doi.org/10.15156/BIO/2938069)"
             shfile = [ "https://figshare.scilifelab.se/ndownloader/files/40788773", "https://figshare.scilifelab.se/ndownloader/files/40788776"]
         }
         'unite-alleuk=9.0' {
             title = "UNITE general FASTA release for eukaryotes - Version 9.0"
-            file = [ "https://files.plutof.ut.ee/public/orig/F2/62/F262D942DEB8CAB3AEB9F313F67B04050E364B72E6707F99755DDCB271C45A48.tgz" ]
-            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2022): UNITE general FASTA release for eukaryotes. Version 16.10.2022. UNITE Community. https://doi.org/10.15156/BIO/2483913"
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/e318f5fd-1ef4-40fd-9e77-1b94d91b3858.tgz" ]
+            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2023): UNITE general FASTA release for eukaryotes. Version 18.07.2023. UNITE Community. https://doi.org/10.15156/BIO/2938069"
             fmtscript = "taxref_reformat_unite.sh"
-            dbversion = "UNITE-alleuk v9.0 (https://doi.org/10.15156/BIO/2483913)"
+            dbversion = "UNITE-alleuk v9.0 (https://doi.org/10.15156/BIO/2938069)"
             shfile = [ "https://figshare.scilifelab.se/ndownloader/files/40788773", "https://figshare.scilifelab.se/ndownloader/files/40788776"]
         }
         'unite-alleuk=8.3' {
             title = "UNITE general FASTA release for eukaryotes - Version 8.3"
-            file = [ "https://files.plutof.ut.ee/public/orig/E5/F5/E5F5E426DEC78BA2F7EC530621DDBD3F10564A09CBC2A5C4D3B3CBE7E37C5E1A.tgz" ]
-            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2021): UNITE general FASTA release for eukaryotes. UNITE Community. 10.15156/BIO/1280127"
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/6e72e839-acfc-4044-84b4-5152b74c1552.tgz" ]
+            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2021): UNITE general FASTA release for eukaryotes. Version 10.05.2021. UNITE Community. https://doi.org/10.15156/BIO/1280127"
             fmtscript = "taxref_reformat_unite.sh"
             dbversion = "UNITE-alleuk v8.3 (https://doi.org/10.15156/BIO/1280127)"
             shfile = [ "https://scilifelab.figshare.com/ndownloader/files/34994575", "https://scilifelab.figshare.com/ndownloader/files/34994578"]
         }
         'unite-alleuk=8.2' {
             title = "UNITE general FASTA release for eukaryotes - Version 8.2"
-            file = [ "https://files.plutof.ut.ee/public/orig/F9/ED/F9EDE36E5209F469056675EBD672425BC06EACB7FE0C0D18F5A13E4CA632DCFA.gz" ]
-            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2020): UNITE general FASTA release for eukaryotes. UNITE Community. 10.15156/BIO/786370"
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/dbd892b6-0446-4351-988e-922c4b73585e.gz" ]
+            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2020): UNITE general FASTA release for eukaryotes. Version 04.02.2020. UNITE Community. https://doi.org/10.15156/BIO/786370"
             fmtscript = "taxref_reformat_unite.sh"
             dbversion = "UNITE-alleuk v8.2 (https://doi.org/10.15156/BIO/786370)"
             shfile = [ "https://scilifelab.figshare.com/ndownloader/files/34994569", "https://scilifelab.figshare.com/ndownloader/files/34994572"]
diff --git a/conf/test_its_dada_taxonomy.config b/conf/test_its_dada_taxonomy.config
new file mode 100644
index 000000000..60ef7a991
--- /dev/null
+++ b/conf/test_its_dada_taxonomy.config
@@ -0,0 +1,50 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/ampliseq -profile test_sintax,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name = 'Test sintax profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function when using sintax for taxonomy assignment'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '12.GB'
+    max_time   = '6.h'
+
+    // Input data
+    FW_primer = "CTTGGTCATTTAGAGGAAGTAA"
+    RV_primer = "TCCTGAGGGAAACTTCG"
+    input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Samplesheet_pacbio_ITS.tsv"
+    metadata = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Metadata_pacbio_ITS.tsv"
+    pacbio = true
+    max_ee = 12
+    cut_its = "its2"
+
+    skip_dada_taxonomy = false
+    dada_ref_taxonomy = "unite-fungi"
+
+    //this is to remove low abundance ASVs to reduce runtime of downstream processes
+    min_samples = 2
+    min_frequency = 10
+
+    //produce average barplots
+    metadata_category_barplot = "var2,var3"
+
+    //restrict ANCOM analysis to higher taxonomic levels
+    tax_agglom_max = 4
+    ancom = true
+
+    sbdiexport = true
+
+    qiime_adonis_formula = "var2"
+
+    diversity_rarefaction_depth = 500
+}
diff --git a/nextflow.config b/nextflow.config
index 7e0a40250..32729b033 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -284,21 +284,22 @@ profiles {
         executor.cpus           = 4
         executor.memory         = 8.GB
     }
-    test               { includeConfig 'conf/test.config'               }
-    test_single        { includeConfig 'conf/test_single.config'        }
-    test_multi         { includeConfig 'conf/test_multi.config'         }
-    test_doubleprimers { includeConfig 'conf/test_doubleprimers.config' }
-    test_pacbio_its    { includeConfig 'conf/test_pacbio_its.config'    }
-    test_iontorrent    { includeConfig 'conf/test_iontorrent.config'    }
-    test_fasta         { includeConfig 'conf/test_fasta.config'         }
-    test_failed        { includeConfig 'conf/test_failed.config'        }
-    test_full          { includeConfig 'conf/test_full.config'          }
-    test_reftaxcustom  { includeConfig 'conf/test_reftaxcustom.config'  }
-    test_qiimecustom   { includeConfig 'conf/test_qiimecustom.config'   }
-    test_novaseq       { includeConfig 'conf/test_novaseq.config'       }
-    test_pplace        { includeConfig 'conf/test_pplace.config'        }
-    test_sintax        { includeConfig 'conf/test_sintax.config'        }
-    test_multiregion   { includeConfig 'conf/test_multiregion.config'   }
+    test                   { includeConfig 'conf/test.config'                   }
+    test_single            { includeConfig 'conf/test_single.config'            }
+    test_multi             { includeConfig 'conf/test_multi.config'             }
+    test_doubleprimers     { includeConfig 'conf/test_doubleprimers.config'     }
+    test_pacbio_its        { includeConfig 'conf/test_pacbio_its.config'        }
+    test_iontorrent        { includeConfig 'conf/test_iontorrent.config'        }
+    test_fasta             { includeConfig 'conf/test_fasta.config'             }
+    test_failed            { includeConfig 'conf/test_failed.config'            }
+    test_full              { includeConfig 'conf/test_full.config'              }
+    test_reftaxcustom      { includeConfig 'conf/test_reftaxcustom.config'      }
+    test_qiimecustom       { includeConfig 'conf/test_qiimecustom.config'       }
+    test_novaseq           { includeConfig 'conf/test_novaseq.config'           }
+    test_pplace            { includeConfig 'conf/test_pplace.config'            }
+    test_sintax            { includeConfig 'conf/test_sintax.config'            }
+    test_its_dada_taxonomy { includeConfig 'conf/test_its_dada_taxonomy.config' }
+    test_multiregion       { includeConfig 'conf/test_multiregion.config'       }
 }
 
 // Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile

From 68d9b2980acfe685866a992a274ac262188d630f Mon Sep 17 00:00:00 2001
From: Daniel Lundin <erik.rikard.daniel@gmail.com>
Date: Wed, 24 Jul 2024 08:56:20 +0200
Subject: [PATCH 04/15] New QIIME/UNITE urls

---
 conf/ref_databases.config | 42 ++++++++++++++++++++++++++++-----------
 nextflow_schema.json      |  7 +++++--
 2 files changed, 35 insertions(+), 14 deletions(-)

diff --git a/conf/ref_databases.config b/conf/ref_databases.config
index 688d571c3..e9037960e 100644
--- a/conf/ref_databases.config
+++ b/conf/ref_databases.config
@@ -298,44 +298,62 @@ params {
         }
         //UNITE for QIIME2, see https://unite.ut.ee/repository.php
         'unite-fungi' {
-            title = "UNITE QIIME release for Fungi - Version 8.3"
-            file = [ "https://files.plutof.ut.ee/public/orig/C5/54/C5547B97AAA979E45F79DC4C8C4B12113389343D7588716B5AD330F8BDB300C9.tgz" ]
-            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2021): UNITE QIIME release for Fungi. Version 10.05.2021. UNITE Community. https://doi.org/10.15156/BIO/1264708"
+            title = "UNITE QIIME release for Fungi - Version 10.0"
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/db1d6ddb-a35d-48c5-8b1a-ad9dd3310c6d.tgz" ]
+            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2024): UNITE QIIME release for Fungi. Version 04.04.2024. UNITE Community. https://doi.org/10.15156/BIO/2959336"
+            fmtscript = "taxref_reformat_qiime_unite.sh"
+        }
+        'unite-fungi=10.0' {
+            title = "UNITE QIIME release for Fungi - Version 10.0"
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/db1d6ddb-a35d-48c5-8b1a-ad9dd3310c6d.tgz" ]
+            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2024): UNITE QIIME release for Fungi. Version 04.04.2024. UNITE Community. https://doi.org/10.15156/BIO/2959336"
+            fmtscript = "taxref_reformat_qiime_unite.sh"
+        }
+        'unite-fungi=9.0' {
+            title = "UNITE QIIME release for Fungi - Version 9.0"
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/3c22fbc5-ed9e-47a6-a85b-6c81268657e9.tgz" ]
+            citation = "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. https://doi.org/10.15156/BIO/2938079"
             fmtscript = "taxref_reformat_qiime_unite.sh"
         }
         'unite-fungi=8.3' {
             title = "UNITE QIIME release for Fungi - Version 8.3"
-            file = [ "https://files.plutof.ut.ee/public/orig/C5/54/C5547B97AAA979E45F79DC4C8C4B12113389343D7588716B5AD330F8BDB300C9.tgz" ]
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/3652451d-7567-4871-a7aa-3ba6c63aa60b.tgz" ]
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2021): UNITE QIIME release for Fungi. Version 10.05.2021. UNITE Community. https://doi.org/10.15156/BIO/1264708"
             fmtscript = "taxref_reformat_qiime_unite.sh"
         }
         'unite-fungi=8.2' {
             title = "UNITE QIIME release for Fungi - Version 8.2"
-            file = [ "https://files.plutof.ut.ee/public/orig/98/AE/98AE96C6593FC9C52D1C46B96C2D9064291F4DBA625EF189FEC1CCAFCF4A1691.gz" ]
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/6b4e0baf-fc68-4e0e-8e4a-f5cf2d68bf98.gz" ]
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2020): UNITE QIIME release for Fungi. Version 04.02.2020. UNITE Community. https://doi.org/10.15156/BIO/786385"
             fmtscript = "taxref_reformat_qiime_unite.sh"
         }
         'unite-alleuk' {
-            title = "UNITE QIIME release for eukaryotes - Version 9.0"
-            file = [ "https://files.plutof.ut.ee/public/orig/8F/FC/8FFCC8A730E50FEEF8CFFEEFEF02A22FBCF7E02B7FD31C6649754834D2CB0E6F.tgz" ]
-            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2022): UNITE QIIME release for eukaryotes. Version 16.10.2022. UNITE Community. https://doi.org/10.15156/BIO/2483917"
+            title = "UNITE QIIME release for eukaryotes - Version 10.0"
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/711a503c-589d-4138-a76f-6a8b89460ecf.tgz" ]
+            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2024): UNITE QIIME release for eukaryotes. Version 04.04.2024. UNITE Community. https://doi.org/10.15156/BIO/2959338"
+            fmtscript = "taxref_reformat_qiime_unite.sh"
+        }
+        'unite-alleuk=10.0' {
+            title = "UNITE QIIME release for eukaryotes - Version 10.0"
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/711a503c-589d-4138-a76f-6a8b89460ecf.tgz" ]
+            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2024): UNITE QIIME release for eukaryotes. Version 04.04.2024. UNITE Community. https://doi.org/10.15156/BIO/2959338"
             fmtscript = "taxref_reformat_qiime_unite.sh"
         }
         'unite-alleuk=9.0' {
             title = "UNITE QIIME release for eukaryotes - Version 9.0"
-            file = [ "https://files.plutof.ut.ee/public/orig/8F/FC/8FFCC8A730E50FEEF8CFFEEFEF02A22FBCF7E02B7FD31C6649754834D2CB0E6F.tgz" ]
-            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2022): UNITE QIIME release for eukaryotes. Version 16.10.2022. UNITE Community. https://doi.org/10.15156/BIO/2483917"
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/ecc2ed00-1219-42c7-a951-fbe92b8cb733.tgz" ]
+            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2023): UNITE QIIME release for eukaryotes. Version 18.07.2023. UNITE Community. https://doi.org/10.15156/BIO/2938081"
             fmtscript = "taxref_reformat_qiime_unite.sh"
         }
         'unite-alleuk=8.3' {
             title = "UNITE QIIME release for eukaryotes - Version 8.3"
-            file = [ "https://files.plutof.ut.ee/public/orig/48/29/4829D91F763E20F0F4376A60AA53FC9FBE6029A7D1BDC1B45347DD64EDE5D560.tgz" ]
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/93683063-613d-4190-877e-26a57a196fc7.tgz" ]
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2021): UNITE QIIME release for eukaryotes. Version 10.05.2021. UNITE Community. https://doi.org/10.15156/BIO/1264819"
             fmtscript = "taxref_reformat_qiime_unite.sh"
         }
         'unite-alleuk=8.2' {
             title = "UNITE QIIME release for eukaryotes - Version 8.2"
-            file = [ "https://files.plutof.ut.ee/public/orig/6E/0E/6E0EDD5592003B47C70A1B384C3C784AA32B726AC861CD7E2BD22AEB0278675E.gz" ]
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/f53a2174-9fc5-4d9f-8230-59f8772c6c5c.gz" ]
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2020): UNITE QIIME release for eukaryotes. Version 04.02.2020. UNITE Community. https://doi.org/10.15156/BIO/786386"
             fmtscript = "taxref_reformat_qiime_unite.sh"
         }
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 32717bcee..35f925ba5 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -457,13 +457,16 @@
                     "enum": [
                         "silva=138",
                         "silva",
+                        "unite-fungi",
+                        "unite-fungi=10.0",
+                        "unite-fungi=9.0",
                         "unite-fungi=8.3",
                         "unite-fungi=8.2",
-                        "unite-fungi",
+                        "unite-alleuk",
+                        "unite-alleuk=10.0",
                         "unite-alleuk=9.0",
                         "unite-alleuk=8.3",
                         "unite-alleuk=8.2",
-                        "unite-alleuk",
                         "greengenes85",
                         "greengenes2",
                         "greengenes2=2022.10"

From 2aae22354f9f609e4d74a17b98e5bdee628bfcb1 Mon Sep 17 00:00:00 2001
From: Daniel Lundin <erik.rikard.daniel@gmail.com>
Date: Wed, 24 Jul 2024 09:01:55 +0200
Subject: [PATCH 05/15] CHANGELOG.md

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 60879ee49..43eb5ab2b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#765](https://github.com/nf-core/ampliseq/pull/765) - Added version R09-RS220 of curated GTDB 16S taxonomy: `sbdi-gtdb=R09-RS220-1` or `sbdi-gtdb` as parameter to `--dada_ref_taxonomy`
+- [#766](https://github.com/nf-core/ampliseq/pull/766) - Added version 10 of Unite as options for `--qiime_ref_taxonomy` and `--sintax_ref_taxonomy`
 
 ### `Changed`
 
@@ -16,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 
 - [#761](https://github.com/nf-core/ampliseq/pull/761) - Some sample sheet checks were not applied due to changes in the metadata ["meta"] structure in version 2.9.0
+- [#766](https://github.com/nf-core/ampliseq/pull/766) - Fixed broken urls for Unite databases (issue [#764](https://github.com/nf-core/ampliseq/issues/764))
 
 ### `Dependencies`
 

From 79297b6091291d7d23476c68561c392d67933424 Mon Sep 17 00:00:00 2001
From: Daniel Lundin <erik.rikard.daniel@gmail.com>
Date: Wed, 24 Jul 2024 11:07:50 +0200
Subject: [PATCH 06/15] Fix duplicate filenames output from QIIME2_ANCOM_TAX

---
 modules/local/qiime2_ancom_tax.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/qiime2_ancom_tax.nf b/modules/local/qiime2_ancom_tax.nf
index 1e3d320bc..e49cfb3ad 100644
--- a/modules/local/qiime2_ancom_tax.nf
+++ b/modules/local/qiime2_ancom_tax.nf
@@ -43,7 +43,7 @@ process QIIME2_ANCOM_TAX {
         --to-tsv
 
     if [ \$(grep -v '^#' -c ${table.baseName}-level-${taxlevel}.feature-table.tsv) -lt 2 ]; then
-        echo ${taxlevel} > ancom/\"WARNING Summing your data at taxonomic level ${taxlevel} produced less than two rows (taxa), ANCOM can't proceed -- did you specify a bad reference taxonomy?\".txt
+        echo ${taxlevel} > ancom/"${table.baseName}_WARNING_Summing_your_data_at_taxonomic_level_${taxlevel}_produced_less_than_two_rows_(taxa)_ANCOM_cant_proceed_--_did_you_specify_a_bad_reference_taxonomy.txt"
     else
         qiime composition add-pseudocount \\
                 --i-table lvl${taxlevel}-${table} \\

From d8a851f47783d9f524fe3ddb831a80b98e0c3cfb Mon Sep 17 00:00:00 2001
From: Daniel Lundin <erik.rikard.daniel@gmail.com>
Date: Wed, 24 Jul 2024 11:23:09 +0200
Subject: [PATCH 07/15] Move table name

---
 modules/local/qiime2_ancom_tax.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/qiime2_ancom_tax.nf b/modules/local/qiime2_ancom_tax.nf
index e49cfb3ad..686a5bace 100644
--- a/modules/local/qiime2_ancom_tax.nf
+++ b/modules/local/qiime2_ancom_tax.nf
@@ -43,7 +43,7 @@ process QIIME2_ANCOM_TAX {
         --to-tsv
 
     if [ \$(grep -v '^#' -c ${table.baseName}-level-${taxlevel}.feature-table.tsv) -lt 2 ]; then
-        echo ${taxlevel} > ancom/"${table.baseName}_WARNING_Summing_your_data_at_taxonomic_level_${taxlevel}_produced_less_than_two_rows_(taxa)_ANCOM_cant_proceed_--_did_you_specify_a_bad_reference_taxonomy.txt"
+        echo ${taxlevel} > ancom/"WARNING_${table.baseName}_Summing_your_data_at_taxonomic_level_${taxlevel}_produced_less_than_two_rows_(taxa)_ANCOM_cant_proceed_--_did_you_specify_a_bad_reference_taxonomy.txt"
     else
         qiime composition add-pseudocount \\
                 --i-table lvl${taxlevel}-${table} \\

From 21f6df83709cea0c91a0205727ec9ca1e54b0382 Mon Sep 17 00:00:00 2001
From: Daniel Lundin <erik.rikard.daniel@gmail.com>
Date: Wed, 24 Jul 2024 12:27:32 +0200
Subject: [PATCH 08/15] More CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 43eb5ab2b..ff7e733a4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Changed`
 
 - [#762](https://github.com/nf-core/ampliseq/pull/762) - Improved output documentation section "Optional ASV filtering" and parameter documentation
+- [#766](https://github.com/nf-core/ampliseq/pull/766) - Modified warning filenames from `QIIME2_ANCOM` to avoid collisions
 
 ### `Fixed`
 

From 9d11568c369533b65ade6895679d2fe703e5de61 Mon Sep 17 00:00:00 2001
From: Daniel Lundin <erik.rikard.daniel@gmail.com>
Date: Wed, 24 Jul 2024 12:27:59 +0200
Subject: [PATCH 09/15] Fixed SINTAX/UNITE urls, tar -> fasta

---
 conf/ref_databases.config | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/conf/ref_databases.config b/conf/ref_databases.config
index e9037960e..73233b72e 100644
--- a/conf/ref_databases.config
+++ b/conf/ref_databases.config
@@ -396,23 +396,23 @@ params {
         }
         'unite-fungi' {
             title = "UNITE USEARCH/UTAX release for Fungi - Version 10.0"
-            file = [ "https://s3.hpc.ut.ee/plutof-public/original/d18aa648-3f4c-4f46-84d4-c8c5d48439ba.tgz" ]
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/b27cffec-1e7d-4584-93d3-12add9fa180b.gz" ]
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2024): UNITE USEARCH/UTAX release for Fungi. UNITE Community. 10.15156/BIO/2959340"
-            fmtscript = "taxref_reformat_sintax_tar.sh"
+            fmtscript = "taxref_reformat_sintax_fasta.sh"
             dbversion = "UNITE-fungi v10.0 (https://doi.plutof.ut.ee/doi/10.15156/BIO/2959340)"
         }
         'unite-fungi=10.0' {
             title = "UNITE USEARCH/UTAX release for Fungi - Version 10.0"
-            file = [ "https://s3.hpc.ut.ee/plutof-public/original/d18aa648-3f4c-4f46-84d4-c8c5d48439ba.tgz" ]
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/b27cffec-1e7d-4584-93d3-12add9fa180b.gz" ]
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2024): UNITE USEARCH/UTAX release for Fungi. UNITE Community. 10.15156/BIO/2959340"
-            fmtscript = "taxref_reformat_sintax_tar.sh"
+            fmtscript = "taxref_reformat_sintax_fasta.sh"
             dbversion = "UNITE-fungi v10.0 (https://doi.plutof.ut.ee/doi/10.15156/BIO/2959340)"
         }
         'unite-fungi=9.0' {
             title = "UNITE USEARCH/UTAX release for Fungi - Version 9.0"
-            file = [ "https://s3.hpc.ut.ee/plutof-public/original/fa1038da-d18d-46b7-88a9-c21bcf38c43d.tgz" ]
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/096d35b9-1d41-42bc-a0a6-dc4f4f17cc79.gz" ]
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2022): UNITE USEARCH/UTAX release for Fungi. Version 16.10.2022. UNITE Community. https://doi.org/10.15156/BIO/2483923"
-            fmtscript = "taxref_reformat_sintax_tar.sh"
+            fmtscript = "taxref_reformat_sintax_fasta.sh"
             dbversion = "UNITE-fungi v9.0 (https://doi.org/10.15156/BIO/2483923)"
         }
         'unite-fungi=8.3' {
@@ -452,9 +452,9 @@ params {
         }
         'unite-alleuk=8.3' {
             title = "UNITE USEARCH/UTAX release for eukaryotes - Version 8.3"
-            file = [ "https://s3.hpc.ut.ee/plutof-public/original/6e72e839-acfc-4044-84b4-5152b74c1552.tgz" ]
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/33ef3b65-5877-4bc9-8210-8e74f5ea63d7.gz" ]
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2021): UNITE USEARCH/UTAX release for eukaryotes. UNITE Community. 10.15156/BIO/1280317"
-            fmtscript = "taxref_reformat_sintax_tar.sh"
+            fmtscript = "taxref_reformat_sintax_fasta.sh"
             dbversion = "UNITE-alleuk v8.3 (https://doi.org/10.15156/BIO/1280127)"
         }
         'unite-alleuk=8.2' {

From 82a5665c9137da7da889dd5e3a6e5627538e8358 Mon Sep 17 00:00:00 2001
From: Daniel Lundin <erik.rikard.daniel@gmail.com>
Date: Wed, 24 Jul 2024 12:56:55 +0200
Subject: [PATCH 10/15] Disable unite-fungi=9.0 -- seems broken at Unite

---
 conf/ref_databases.config | 3 +++
 nextflow_schema.json      | 1 -
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/conf/ref_databases.config b/conf/ref_databases.config
index 73233b72e..619448051 100644
--- a/conf/ref_databases.config
+++ b/conf/ref_databases.config
@@ -309,12 +309,15 @@ params {
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2024): UNITE QIIME release for Fungi. Version 04.04.2024. UNITE Community. https://doi.org/10.15156/BIO/2959336"
             fmtscript = "taxref_reformat_qiime_unite.sh"
         }
+        // This fails, and is therefore commented out. The error message is: "this classifier does not support confidence values"
+        /***
         'unite-fungi=9.0' {
             title = "UNITE QIIME release for Fungi - Version 9.0"
             file = [ "https://s3.hpc.ut.ee/plutof-public/original/3c22fbc5-ed9e-47a6-a85b-6c81268657e9.tgz" ]
             citation = "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. https://doi.org/10.15156/BIO/2938079"
             fmtscript = "taxref_reformat_qiime_unite.sh"
         }
+        ***/
         'unite-fungi=8.3' {
             title = "UNITE QIIME release for Fungi - Version 8.3"
             file = [ "https://s3.hpc.ut.ee/plutof-public/original/3652451d-7567-4871-a7aa-3ba6c63aa60b.tgz" ]
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 35f925ba5..92f0fdc18 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -459,7 +459,6 @@
                         "silva",
                         "unite-fungi",
                         "unite-fungi=10.0",
-                        "unite-fungi=9.0",
                         "unite-fungi=8.3",
                         "unite-fungi=8.2",
                         "unite-alleuk",

From 5fde4547365127c3d76705f571bc6383b0066e52 Mon Sep 17 00:00:00 2001
From: Daniel Lundin <erik.rikard.daniel@gmail.com>
Date: Wed, 24 Jul 2024 13:13:59 +0200
Subject: [PATCH 11/15] Warning in bin/taxref_reformat_sintax_tar.sh

---
 bin/taxref_reformat_sintax_tar.sh | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/bin/taxref_reformat_sintax_tar.sh b/bin/taxref_reformat_sintax_tar.sh
index 8539084d9..f8a3e4230 100755
--- a/bin/taxref_reformat_sintax_tar.sh
+++ b/bin/taxref_reformat_sintax_tar.sh
@@ -1,9 +1,8 @@
 #!/bin/sh
 
-# Handles preformatted database files suitable for sintax
-
-# Just rename the preformatted file
-# Assumes only one (gzipped) file
+# Handles preformatted database tar files suitable for sintax
+#
+# This turned out to be a MISTAKE and is NOT USED, but I'm keeping the file for a while anyway.
 
 # Extract the fasta file without _dev in its name
 f=$(tar tfz *.tgz | grep fasta | grep -v '_dev')

From 9a8094d5cb144a310bcc981cfb2cc355241647d6 Mon Sep 17 00:00:00 2001
From: Daniel Lundin <erik.rikard.daniel@gmail.com>
Date: Wed, 24 Jul 2024 15:45:15 +0200
Subject: [PATCH 12/15] Revert most of the filename changes in QIIME2_ANCOM_TAX

---
 modules/local/qiime2_ancom_tax.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/qiime2_ancom_tax.nf b/modules/local/qiime2_ancom_tax.nf
index 686a5bace..cf4882764 100644
--- a/modules/local/qiime2_ancom_tax.nf
+++ b/modules/local/qiime2_ancom_tax.nf
@@ -43,7 +43,7 @@ process QIIME2_ANCOM_TAX {
         --to-tsv
 
     if [ \$(grep -v '^#' -c ${table.baseName}-level-${taxlevel}.feature-table.tsv) -lt 2 ]; then
-        echo ${taxlevel} > ancom/"WARNING_${table.baseName}_Summing_your_data_at_taxonomic_level_${taxlevel}_produced_less_than_two_rows_(taxa)_ANCOM_cant_proceed_--_did_you_specify_a_bad_reference_taxonomy.txt"
+        echo ${taxlevel} > ancom/\"WARNING ${table.baseName} Summing your data at taxonomic level ${taxlevel} produced less than two rows (taxa), ANCOM can't proceed -- did you specify a bad reference taxonomy?\".txt
     else
         qiime composition add-pseudocount \\
                 --i-table lvl${taxlevel}-${table} \\

From 641fc4c52fedeb05cb2db2592fe572111b4071dd Mon Sep 17 00:00:00 2001
From: Daniel Lundin <erik.rikard.daniel@gmail.com>
Date: Wed, 24 Jul 2024 16:31:51 +0200
Subject: [PATCH 13/15] Disable Unite databases for --qiime_ref_taxonomy

---
 CHANGELOG.md              | 3 ++-
 conf/ref_databases.config | 9 +++++++--
 nextflow_schema.json      | 9 ---------
 3 files changed, 9 insertions(+), 12 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ff7e733a4..5f6f1aca1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,12 +8,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#765](https://github.com/nf-core/ampliseq/pull/765) - Added version R09-RS220 of curated GTDB 16S taxonomy: `sbdi-gtdb=R09-RS220-1` or `sbdi-gtdb` as parameter to `--dada_ref_taxonomy`
-- [#766](https://github.com/nf-core/ampliseq/pull/766) - Added version 10 of Unite as options for `--qiime_ref_taxonomy` and `--sintax_ref_taxonomy`
+- [#766](https://github.com/nf-core/ampliseq/pull/766) - Added version 10 of Unite as options for `--sintax_ref_taxonomy`
 
 ### `Changed`
 
 - [#762](https://github.com/nf-core/ampliseq/pull/762) - Improved output documentation section "Optional ASV filtering" and parameter documentation
 - [#766](https://github.com/nf-core/ampliseq/pull/766) - Modified warning filenames from `QIIME2_ANCOM` to avoid collisions
+- [#766](https://github.com/nf-core/ampliseq/pull/766) - Disabled Unite databases from the `--qiime_ref_taxonomy` because of divergent results compared to the other classifiers
 
 ### `Fixed`
 
diff --git a/conf/ref_databases.config b/conf/ref_databases.config
index 619448051..b91ea8ea7 100644
--- a/conf/ref_databases.config
+++ b/conf/ref_databases.config
@@ -309,7 +309,12 @@ params {
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2024): UNITE QIIME release for Fungi. Version 04.04.2024. UNITE Community. https://doi.org/10.15156/BIO/2959336"
             fmtscript = "taxref_reformat_qiime_unite.sh"
         }
-        // This fails, and is therefore commented out. The error message is: "this classifier does not support confidence values"
+
+        // We have disabled all Unite databases for the QIIME2 classifiers
+        // since we get results that differ considerably from the Sintax and
+        // DADA2 classifiers with the corresponding databases.
+
+        // The unite-fungi=9.0 fails
         /***
         'unite-fungi=9.0' {
             title = "UNITE QIIME release for Fungi - Version 9.0"
@@ -317,7 +322,6 @@ params {
             citation = "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. https://doi.org/10.15156/BIO/2938079"
             fmtscript = "taxref_reformat_qiime_unite.sh"
         }
-        ***/
         'unite-fungi=8.3' {
             title = "UNITE QIIME release for Fungi - Version 8.3"
             file = [ "https://s3.hpc.ut.ee/plutof-public/original/3652451d-7567-4871-a7aa-3ba6c63aa60b.tgz" ]
@@ -360,6 +364,7 @@ params {
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2020): UNITE QIIME release for eukaryotes. Version 04.02.2020. UNITE Community. https://doi.org/10.15156/BIO/786386"
             fmtscript = "taxref_reformat_qiime_unite.sh"
         }
+        ***/
         'greengenes85' {
             title = "Greengenes 16S - Version 13_8 - clustered at 85% similarity - for testing purposes only"
             file = [ "https://data.qiime2.org/2023.7/tutorials/training-feature-classifiers/85_otus.fasta", "https://data.qiime2.org/2023.7/tutorials/training-feature-classifiers/85_otu_taxonomy.txt" ]
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 92f0fdc18..8df67e3ce 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -457,15 +457,6 @@
                     "enum": [
                         "silva=138",
                         "silva",
-                        "unite-fungi",
-                        "unite-fungi=10.0",
-                        "unite-fungi=8.3",
-                        "unite-fungi=8.2",
-                        "unite-alleuk",
-                        "unite-alleuk=10.0",
-                        "unite-alleuk=9.0",
-                        "unite-alleuk=8.3",
-                        "unite-alleuk=8.2",
                         "greengenes85",
                         "greengenes2",
                         "greengenes2=2022.10"

From 1d697626c272c1ec99092c94242f4381ec110664 Mon Sep 17 00:00:00 2001
From: Daniel Lundin <erik.rikard.daniel@gmail.com>
Date: Wed, 24 Jul 2024 19:10:45 +0200
Subject: [PATCH 14/15] prettier

---
 .devcontainer/devcontainer.json | 8 ++++----
 nextflow_schema.json            | 8 +-------
 2 files changed, 5 insertions(+), 11 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index b290e0901..2a997736a 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -10,11 +10,11 @@
         "vscode": {
             // Set *default* container specific settings.json values on container create.
             "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python"
+                "python.defaultInterpreterPath": "/opt/conda/bin/python",
             },
 
             // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
-        }
-    }
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"],
+        },
+    },
 }
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 8df67e3ce..ccef5f95f 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -454,13 +454,7 @@
                     "type": "string",
                     "help_text": "Choose any of the supported databases, and optionally also specify the version. Database and version are separated by an equal sign (`=`, e.g. `silva=138`) . This will download the desired database and initiate taxonomic classification with QIIME2 and the chosen database.\n\nIf both, `--dada_ref_taxonomy` and `--qiime_ref_taxonomy` are used, DADA2 classification will be used for downstream analysis.\n\nThe following databases are supported:\n- SILVA ribosomal RNA gene database project - 16S rRNA\n- UNITE - eukaryotic nuclear ribosomal ITS region - ITS\n- Greengenes (only testing!)\n\nGenerally, using `silva`, `unite-fungi`, or `unite-alleuk` will select the most recent supported version. For testing purposes, the tiny database `greengenes85` (dereplicated at 85% sequence similarity) is available. For details on what values are valid, please either use an invalid value such as `x` (causing the pipeline to send an error message with all valid values) or see `conf/ref_databases.config`.",
                     "description": "Name of supported database, and optionally also version number",
-                    "enum": [
-                        "silva=138",
-                        "silva",
-                        "greengenes85",
-                        "greengenes2",
-                        "greengenes2=2022.10"
-                    ]
+                    "enum": ["silva=138", "silva", "greengenes85", "greengenes2", "greengenes2=2022.10"]
                 },
                 "qiime_ref_tax_custom": {
                     "type": "string",

From 8e9b28d0fde5e29a8f83351e552497cb86e80a15 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 24 Jul 2024 17:24:23 +0000
Subject: [PATCH 15/15] [automated] Fix code linting

---
 .devcontainer/devcontainer.json | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 2a997736a..b290e0901 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -10,11 +10,11 @@
         "vscode": {
             // Set *default* container specific settings.json values on container create.
             "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python",
+                "python.defaultInterpreterPath": "/opt/conda/bin/python"
             },
 
             // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"],
-        },
-    },
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
+        }
+    }
 }