Merge pull request #797 from d4straub/update-qiime-2023.7-2024.10

Update QIIME2 from 2023.7 to 2024.10
nf-core · Nov 20, 2024 · 3eb037c · 3eb037c
2 parents 4052833 + 13782d5
commit 3eb037c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,6 +13,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `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
@@ -282,6 +282,7 @@ 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)