Merge branch 'dev' into consensus-pr

nf-core · Nov 21, 2024 · c3e4165 · c3e4165
2 parents a9ed8c4 + b350380
commit c3e4165
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#804](https://github.com/nf-core/ampliseq/pull/804) - Added version 10 of Unite as parameter for `--dada_ref_taxonomy` (issue [#768](https://github.com/nf-core/ampliseq/issues/768))
 - [#803](https://github.com/nf-core/ampliseq/pull/803) - New parameters introduced related to `--mergepairs_strategy`. These parameters would only be effective if `--mergepairs_strategy consensus` is set.
 
 | **Parameter**                              | **Description**                                                                           | **Default Value** |
@@ -17,13 +18,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | **mergepairs_consensus_minoverlap**        | The minimum number of overlapping base pairs required to merge forward and reverse reads. | 12                |
 | **mergepairs_consensus_maxmismatch**       | The maximum number of mismatches allowed within the overlapping region for merging reads. | 0                 |
 | **mergepairs_consensus_percentile_cutoff** | The percentile cutoff determining the minimum observed overlap in the dataset.            | 0.001             |
+=======
 
 ### `Changed`
 
 - [#803](https://github.com/nf-core/ampliseq/pull/803) - Changed DADA2_DENOISING : `--concatenate_reads` renaming to `--mergepairs_strategy` ; support new method named "consensus" by setting `--mergepairs_strategy consensus` ; changed options of `--mergepairs_strategy` from TRUE/FALSE (boolean) to ["merge", "concatenate", "consensus"].
 
 ### `Fixed`
 
+- [#800](https://github.com/nf-core/ampliseq/pull/800) - Fixed SH files for UNITE9.0, they were missing some entries due to a bug caused by API update in PlutoF
+
 ### `Dependencies`
 
 - [#797](https://github.com/nf-core/ampliseq/pull/797) - Update QIIME2

diff --git a/conf/ref_databases.config b/conf/ref_databases.config
@@ -199,20 +199,28 @@ params {
             dbversion = "SILVA v132 (https://zenodo.org/record/1172783)"
         }
         '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 (2023): UNITE general FASTA release for Fungi. Version 18.07.2023. UNITE Community. https://doi.org/10.15156/BIO/2938067"
+            title = "UNITE general FASTA 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 general FASTA release for Fungi. Version 04.04.2024. UNITE Community. https://doi.org/10.15156/BIO/2959332"
             fmtscript = "taxref_reformat_unite.sh"
-            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"]
+            dbversion = "UNITE-fungi v10.0 (https://doi.org/10.15156/BIO/2959332)"
+            shfile = [ "https://figshare.scilifelab.se/ndownloader/files/50595459", "https://figshare.scilifelab.se/ndownloader/files/50595462"]
+        }
+        'unite-fungi=10.0' {
+            title = "UNITE general FASTA 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 general FASTA release for Fungi. Version 04.04.2024. UNITE Community. https://doi.org/10.15156/BIO/2959332"
+            fmtscript = "taxref_reformat_unite.sh"
+            dbversion = "UNITE-fungi v10.0 (https://doi.org/10.15156/BIO/2959332)"
+            shfile = [ "https://figshare.scilifelab.se/ndownloader/files/50595459", "https://figshare.scilifelab.se/ndownloader/files/50595462"]
         }
         '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 (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/2938067)"
-            shfile = [ "https://figshare.scilifelab.se/ndownloader/files/40788767", "https://figshare.scilifelab.se/ndownloader/files/40788770"]
+            shfile = [ "https://figshare.scilifelab.se/ndownloader/files/50055762", "https://figshare.scilifelab.se/ndownloader/files/50055765"]
         }
         'unite-fungi=8.3' {
             title = "UNITE general FASTA release for Fungi - Version 8.3"
@@ -231,20 +239,28 @@ params {
             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://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"
+            title = "UNITE general FASTA release for eukaryotes - Version 10.0"
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/1dda2021-4893-4f2f-b50e-87bfea795267.tgz" ]
+            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2024): UNITE general FASTA release for eukaryotes. Version 04.04.2024. UNITE Community. https://doi.org/10.15156/BIO/2959334"
             fmtscript = "taxref_reformat_unite.sh"
-            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"]
+            dbversion = "UNITE-alleuk v10.0 (https://doi.org/10.15156/BIO/2959334)"
+            shfile = [ "https://figshare.scilifelab.se/ndownloader/files/50595465", "https://figshare.scilifelab.se/ndownloader/files/50595471"]
+        }
+        'unite-alleuk=10.0' {
+            title = "UNITE general FASTA release for eukaryotes - Version 10.0"
+            file = [ "https://s3.hpc.ut.ee/plutof-public/original/1dda2021-4893-4f2f-b50e-87bfea795267.tgz" ]
+            citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2024): UNITE general FASTA release for eukaryotes. Version 04.04.2024. UNITE Community. https://doi.org/10.15156/BIO/2959334"
+            fmtscript = "taxref_reformat_unite.sh"
+            dbversion = "UNITE-alleuk v10.0 (https://doi.org/10.15156/BIO/2959334)"
+            shfile = [ "https://figshare.scilifelab.se/ndownloader/files/50595465", "https://figshare.scilifelab.se/ndownloader/files/50595471"]
         }
         'unite-alleuk=9.0' {
             title = "UNITE general FASTA release for eukaryotes - Version 9.0"
             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/2938069)"
-            shfile = [ "https://figshare.scilifelab.se/ndownloader/files/40788773", "https://figshare.scilifelab.se/ndownloader/files/40788776"]
+            shfile = [ "https://figshare.scilifelab.se/ndownloader/files/50055768", "https://figshare.scilifelab.se/ndownloader/files/50055771"]
         }
         'unite-alleuk=8.3' {
             title = "UNITE general FASTA release for eukaryotes - Version 8.3"

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -428,10 +428,12 @@
                         "silva=132",
                         "silva=138",
                         "unite-alleuk",
+                        "unite-alleuk=10.0",
                         "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",