Merge branch 'dev' into add-dada2-silva-138.2

nf-core · Nov 21, 2024 · 02d019f · 02d019f
2 parents bc8b146 + b350380
commit 02d019f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,13 +8,22 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#798](https://github.com/nf-core/ampliseq/pull/798) - Added SILVA version 138.2 of DADA2 taxonomy database: `silva=138.2` or `silva` as parameter to `--dada2_ref_taxonomy`
+- [#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))
 
 ### `Changed`
 
 ### `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
+
+| software | previously | now     |
+| -------- | ---------- | ------- |
+| QIIME2   | 2023.7     | 2024.10 |
+
 ### `Removed`
 
 ## nf-core/ampliseq version 2.12.0 - 2024-11-14

diff --git a/conf/ref_databases.config b/conf/ref_databases.config
@@ -206,20 +206,28 @@ 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"
@@ -238,20 +246,28 @@ 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"
@@ -289,6 +305,7 @@ params {
     //QIIME2 taxonomic reference databases
     qiime_ref_databases {
         //SILVA for QIIME2 v2023.7, see https://docs.qiime2.org/2023.7/data-resources/#silva-16s-18s-rrna
+        //SILVA for QIIME2 v2023.7 md5sums identical to QIIME2 v2024.10, but links on https://docs.qiime2.org/2024.10/data-resources/ are failing
         'silva=138' {
             title = "QIIME2 pre-formatted SILVA dereplicated at 99% similarity - Version 138"
             file = [ "https://data.qiime2.org/2023.7/common/silva-138-99-seqs.qza", "https://data.qiime2.org/2023.7/common/silva-138-99-tax.qza" ]

diff --git a/modules/local/qiime2_alphararefaction.nf b/modules/local/qiime2_alphararefaction.nf
@@ -1,7 +1,7 @@
 process QIIME2_ALPHARAREFACTION {
     label 'process_low'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     path(metadata)

diff --git a/modules/local/qiime2_ancom_asv.nf b/modules/local/qiime2_ancom_asv.nf
@@ -5,7 +5,7 @@ process QIIME2_ANCOM_ASV {
     label 'process_long'
     label 'error_ignore'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     tuple path(metadata), path(table)

diff --git a/modules/local/qiime2_ancom_tax.nf b/modules/local/qiime2_ancom_tax.nf
@@ -3,7 +3,7 @@ process QIIME2_ANCOM_TAX {
     label 'process_medium'
     label 'single_cpu'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     tuple path(metadata), path(table), path(taxonomy) ,val(taxlevel)

diff --git a/modules/local/qiime2_ancombc_asv.nf b/modules/local/qiime2_ancombc_asv.nf
@@ -5,7 +5,7 @@ process QIIME2_ANCOMBC_ASV {
     label 'process_long'
     label 'error_ignore'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     tuple path(metadata), path(table), val(formula)

diff --git a/modules/local/qiime2_ancombc_tax.nf b/modules/local/qiime2_ancombc_tax.nf
@@ -3,7 +3,7 @@ process QIIME2_ANCOMBC_TAX {
     label 'process_medium'
     label 'single_cpu'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     tuple path(metadata), path(table), path(taxonomy), val(taxlevel), val(formula)

diff --git a/modules/local/qiime2_barplot.nf b/modules/local/qiime2_barplot.nf
@@ -1,7 +1,7 @@
 process QIIME2_BARPLOT {
     label 'process_low'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     path(metadata)

diff --git a/modules/local/qiime2_classify.nf b/modules/local/qiime2_classify.nf
@@ -2,7 +2,7 @@ process QIIME2_CLASSIFY {
     tag "${repseq},${trained_classifier}"
     label 'process_high'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     path(trained_classifier)

diff --git a/modules/local/qiime2_diversity_adonis.nf b/modules/local/qiime2_diversity_adonis.nf
@@ -2,7 +2,7 @@ process QIIME2_DIVERSITY_ADONIS {
     tag "${core.baseName}-${formula}"
     label 'process_low'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     tuple path(metadata), path(core), val(formula)

diff --git a/modules/local/qiime2_diversity_alpha.nf b/modules/local/qiime2_diversity_alpha.nf
@@ -2,7 +2,7 @@ process QIIME2_DIVERSITY_ALPHA {
     tag "${core.baseName}"
     label 'process_low'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     tuple path(metadata), path(core)

diff --git a/modules/local/qiime2_diversity_beta.nf b/modules/local/qiime2_diversity_beta.nf
@@ -2,7 +2,7 @@ process QIIME2_DIVERSITY_BETA {
     tag "${core.baseName}-${category}"
     label 'process_low'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     tuple path(metadata), path(core), val(category)

diff --git a/modules/local/qiime2_diversity_betaord.nf b/modules/local/qiime2_diversity_betaord.nf
@@ -2,7 +2,7 @@ process QIIME2_DIVERSITY_BETAORD {
     tag "${core.baseName}"
     label 'process_low'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     tuple path(metadata), path(core)

diff --git a/modules/local/qiime2_diversity_core.nf b/modules/local/qiime2_diversity_core.nf
@@ -1,7 +1,7 @@
 process QIIME2_DIVERSITY_CORE {
     label 'process_low'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     path(metadata)

diff --git a/modules/local/qiime2_export_absolute.nf b/modules/local/qiime2_export_absolute.nf
@@ -1,7 +1,7 @@
 process QIIME2_EXPORT_ABSOLUTE {
     label 'process_low'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     path(table)

diff --git a/modules/local/qiime2_export_relasv.nf b/modules/local/qiime2_export_relasv.nf
@@ -1,7 +1,7 @@
 process QIIME2_EXPORT_RELASV {
     label 'process_low'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     path(table)

diff --git a/modules/local/qiime2_export_reltax.nf b/modules/local/qiime2_export_reltax.nf
@@ -1,7 +1,7 @@
 process QIIME2_EXPORT_RELTAX {
     label 'process_low'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     path(table)

diff --git a/modules/local/qiime2_extract.nf b/modules/local/qiime2_extract.nf
@@ -1,7 +1,7 @@
 process QIIME2_EXTRACT {
     tag "${meta.FW_primer}-${meta.RV_primer}"
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     tuple val(meta), path(database)

diff --git a/modules/local/qiime2_featuretable_group.nf b/modules/local/qiime2_featuretable_group.nf
@@ -2,7 +2,7 @@ process QIIME2_FEATURETABLE_GROUP {
     tag "${category}"
     label 'process_low'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     tuple path(table), path(metadata), val(category)

diff --git a/modules/local/qiime2_filtersamples.nf b/modules/local/qiime2_filtersamples.nf
@@ -2,7 +2,7 @@ process QIIME2_FILTERSAMPLES {
     tag "${filter}"
     label 'process_low'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     tuple path(metadata), path(table), val(filter)

diff --git a/modules/local/qiime2_inasv.nf b/modules/local/qiime2_inasv.nf
@@ -2,7 +2,7 @@ process QIIME2_INASV {
     tag "${asv}"
     label 'process_low'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     path(asv)

diff --git a/modules/local/qiime2_inseq.nf b/modules/local/qiime2_inseq.nf
@@ -2,7 +2,7 @@ process QIIME2_INSEQ {
     tag "${seq}"
     label 'process_low'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     path(seq)

diff --git a/modules/local/qiime2_intax.nf b/modules/local/qiime2_intax.nf
@@ -2,7 +2,7 @@ process QIIME2_INTAX {
     tag "${tax}"
     label 'process_low'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     path(tax) //ASV_tax_species.tsv

diff --git a/modules/local/qiime2_intree.nf b/modules/local/qiime2_intree.nf
@@ -2,7 +2,7 @@ process QIIME2_INTREE {
     tag "${meta.id}:${meta.model}"
     label 'process_low'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     tuple val(meta), path(tree)

diff --git a/modules/local/qiime2_seqfiltertable.nf b/modules/local/qiime2_seqfiltertable.nf
@@ -2,7 +2,7 @@ process QIIME2_SEQFILTERTABLE {
     tag "${repseq}-filter-by-${table}"
     label 'process_low'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     path(table)

diff --git a/modules/local/qiime2_tablefiltertaxa.nf b/modules/local/qiime2_tablefiltertaxa.nf
@@ -2,7 +2,7 @@ process QIIME2_TABLEFILTERTAXA {
     tag "taxa:${exclude_taxa};min-freq:${min_frequency};min-samples:${min_samples}"
     label 'process_low'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     path(table)

diff --git a/modules/local/qiime2_train.nf b/modules/local/qiime2_train.nf
@@ -3,7 +3,7 @@ process QIIME2_TRAIN {
     label 'process_high'
     label 'single_cpu'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     tuple val(meta), path(qza)

diff --git a/modules/local/qiime2_tree.nf b/modules/local/qiime2_tree.nf
@@ -1,7 +1,7 @@
 process QIIME2_TREE {
     label 'process_medium'
 
-    container "qiime2/core:2023.7"
+    container "qiime2/amplicon:2024.10"
 
     input:
     path(repseq)

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -382,10 +382,12 @@
                         "silva=138",
                         "silva=132",
                         "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",