nf-core · d4straub · Oct 17, 2023 · Oct 16, 2023 · Oct 16, 2023 · Oct 16, 2023
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -40,6 +40,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Dependencies`
 
+- [#646](https://github.com/nf-core/ampliseq/pull/646) - Updated dependencies, see below:
+
+| software | previously | now    |
+| -------- | ---------- | ------ |
+| FASTQC   | 0.11.9     | 0.12.1 |
+| DADA2    | 1.22.0     | 1.28.0 |
+| PICRUSt2 | 2.5.0      | 2.5.2  |
+| QIIME2   | 2022.11    | 2023.7 |
+
 ### `Removed`
 
 ## nf-core/ampliseq version 2.6.1 - 2023-06-28

diff --git a/conf/ref_databases.config b/conf/ref_databases.config
@@ -242,17 +242,17 @@ params {
     }
     //QIIME2 taxonomic reference databases
     qiime_ref_databases {
-        //SILVA for QIIME2 v2021.2, see https://docs.qiime2.org/2021.2/data-resources/#silva-16s-18s-rrna
+        //SILVA for QIIME2 v2023.7, see https://docs.qiime2.org/2023.7/data-resources/#silva-16s-18s-rrna
         'silva=138' {
             title = "QIIME2 pre-formatted SILVA dereplicated at 99% similarity - Version 138"
-            file = [ "https://data.qiime2.org/2022.11/common/silva-138-99-seqs.qza", "https://data.qiime2.org/2022.11/common/silva-138-99-tax.qza" ]
+            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" ]
             citation = "https://www.arb-silva.de/; Bokulich, N.A., Robeson, M., Dillon, M.R. bokulich-lab/RESCRIPt. Zenodo. http://doi.org/10.5281/zenodo.3891931"
             license = "https://www.arb-silva.de/silva-license-information/"
             fmtscript = "taxref_reformat_qiime_silva138.sh"
         }
         'silva' {
             title = "QIIME2 pre-formatted SILVA dereplicated at 99% similarity - Version 138"
-            file = [ "https://data.qiime2.org/2022.11/common/silva-138-99-seqs.qza", "https://data.qiime2.org/2022.11/common/silva-138-99-tax.qza" ]
+            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" ]
             citation = "https://www.arb-silva.de/; Bokulich, N.A., Robeson, M., Dillon, M.R. bokulich-lab/RESCRIPt. Zenodo. http://doi.org/10.5281/zenodo.3891931"
             license = "https://www.arb-silva.de/silva-license-information/"
             fmtscript = "taxref_reformat_qiime_silva138.sh"
@@ -302,7 +302,7 @@ params {
         }
         'greengenes85' {
             title = "Greengenes 16S - Version 13_8 - clustered at 85% similarity - for testing purposes only"
-            file = [ "https://data.qiime2.org/2022.11/tutorials/training-feature-classifiers/85_otus.fasta", "https://data.qiime2.org/2022.11/tutorials/training-feature-classifiers/85_otu_taxonomy.txt" ]
+            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" ]
             citation = "McDonald, D., Price, M., Goodrich, J. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6, 610–618 (2012). https://doi.org/10.1038/ismej.2011.139"
             fmtscript = "taxref_reformat_qiime_greengenes85.sh"
         }

diff --git a/modules.json b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0",
                         "installed_by": ["modules"]
                     },
                     "cutadapt": {
@@ -27,7 +27,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
+                        "git_sha": "c7494026693ba1a7db683e1520816709db3f05a0",
                         "installed_by": ["modules"]
                     },
                     "gappa/examineassign": {
@@ -73,12 +73,12 @@
                     },
                     "mafft": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "feb29be775d9e41750180539e9a3bdce801d0609",
                         "installed_by": ["fasta_newick_epang_gappa"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
                         "installed_by": ["modules"]
                     },
                     "untar": {
@@ -107,7 +107,7 @@
                 "nf-core": {
                     "fasta_newick_epang_gappa": {
                         "branch": "master",
-                        "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
+                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
                         "installed_by": ["subworkflows"]
                     }
                 }

diff --git a/modules/local/cutadapt_summary_merge.nf b/modules/local/cutadapt_summary_merge.nf
@@ -2,10 +2,10 @@ process CUTADAPT_SUMMARY_MERGE {
     tag "${files}"
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
+    conda "bioconda::bioconductor-dada2=1.28.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
-        'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
 
     input:
     val(action)

diff --git a/modules/local/dada2_addspecies.nf b/modules/local/dada2_addspecies.nf
@@ -3,10 +3,10 @@ process DADA2_ADDSPECIES {
     label 'process_high'
     label 'single_cpu'
 
-    conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
+    conda "bioconda::bioconductor-dada2=1.28.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
-        'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
 
     input:
     path(taxtable)

diff --git a/modules/local/dada2_denoising.nf b/modules/local/dada2_denoising.nf
@@ -3,10 +3,10 @@ process DADA2_DENOISING {
     label 'process_medium'
     label 'process_long'
 
-    conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
+    conda "bioconda::bioconductor-dada2=1.28.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
-        'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
 
     input:
     tuple val(meta), path("filtered/*"), path(errormodel)

diff --git a/modules/local/dada2_err.nf b/modules/local/dada2_err.nf
@@ -2,10 +2,10 @@ process DADA2_ERR {
     tag "$meta.run"
     label 'process_medium'
 
-    conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
+    conda "bioconda::bioconductor-dada2=1.28.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
-        'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
 
     input:
     tuple val(meta), path(reads)

diff --git a/modules/local/dada2_filtntrim.nf b/modules/local/dada2_filtntrim.nf
@@ -2,10 +2,10 @@ process DADA2_FILTNTRIM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
+    conda "bioconda::bioconductor-dada2=1.28.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
-        'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
 
     input:
     tuple val(meta), path(reads), val(trunclenf), val(trunclenr)

diff --git a/modules/local/dada2_merge.nf b/modules/local/dada2_merge.nf
@@ -1,6 +1,7 @@
 process DADA2_MERGE {
     label 'process_low'
 
+    // https://depot.galaxyproject.org/singularity/bioconductor-dada2=1.28.0--r43hf17093f_0 doesnt contain 'digest', so keep here v1.22.0
     conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :

diff --git a/modules/local/dada2_quality.nf b/modules/local/dada2_quality.nf
@@ -2,10 +2,10 @@ process DADA2_QUALITY {
     tag "$meta"
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
+    conda "bioconda::bioconductor-dada2=1.28.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
-        'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
 
     input:
     tuple val(meta), path(reads)

diff --git a/modules/local/dada2_rmchimera.nf b/modules/local/dada2_rmchimera.nf
@@ -2,10 +2,10 @@ process DADA2_RMCHIMERA {
     tag "$meta.run"
     label 'process_medium'
 
-    conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
+    conda "bioconda::bioconductor-dada2=1.28.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
-        'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
 
     input:
     tuple val(meta), path(seqtab)

diff --git a/modules/local/dada2_stats.nf b/modules/local/dada2_stats.nf
@@ -2,10 +2,10 @@ process DADA2_STATS {
     tag "$meta.run"
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
+    conda "bioconda::bioconductor-dada2=1.28.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
-        'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
 
     input:
     tuple val(meta), path("filter_and_trim_files/*"), path(denoised), path(mergers), path(seqtab_nochim)

diff --git a/modules/local/dada2_taxonomy.nf b/modules/local/dada2_taxonomy.nf
@@ -2,10 +2,10 @@ process DADA2_TAXONOMY {
     tag "${fasta},${database}"
     label 'process_high'
 
-    conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
+    conda "bioconda::bioconductor-dada2=1.28.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
-        'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
 
     input:
     path(fasta)

diff --git a/modules/local/format_pplacetax.nf b/modules/local/format_pplacetax.nf
@@ -2,10 +2,10 @@ process FORMAT_PPLACETAX {
     tag "${tax.baseName}"
     label 'process_high'
 
-    conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
+    conda "bioconda::bioconductor-dada2=1.28.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
-        'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
 
     input:
     tuple val(meta), path(tax)

diff --git a/modules/local/merge_stats.nf b/modules/local/merge_stats.nf
@@ -1,10 +1,10 @@
 process MERGE_STATS {
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
+    conda "bioconda::bioconductor-dada2=1.28.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
-        'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
 
     input:
     path('file1.tsv')

diff --git a/modules/local/metadata_all.nf b/modules/local/metadata_all.nf
@@ -2,10 +2,10 @@ process METADATA_ALL {
     tag "$metadata"
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
+    conda "bioconda::bioconductor-dada2=1.28.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
-        'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
 
     input:
     path(metadata)

diff --git a/modules/local/metadata_pairwise.nf b/modules/local/metadata_pairwise.nf
@@ -2,10 +2,10 @@ process METADATA_PAIRWISE {
     tag "$metadata"
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
+    conda "bioconda::bioconductor-dada2=1.28.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
-        'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
 
     input:
     path(metadata)

diff --git a/modules/local/novaseq_err.nf b/modules/local/novaseq_err.nf
@@ -2,10 +2,10 @@ process NOVASEQ_ERR {
     tag "$meta.run"
     label 'process_medium'
 
-    conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
+    conda "bioconda::bioconductor-dada2=1.28.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
-        'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
+        'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
+        'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
 
     input:
     tuple val(meta), path(errormodel)

diff --git a/modules/local/picrust.nf b/modules/local/picrust.nf
@@ -2,10 +2,10 @@ process PICRUST {
     tag "${seq},${abund}"
     label 'process_medium'
 
-    conda "bioconda::picrust2=2.5.0"
+    conda "bioconda::picrust2=2.5.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picrust2:2.5.0--pyhdfd78af_0' :
-        'biocontainers/picrust2:2.5.0--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picrust2:2.5.2--pyhdfd78af_0' :
+        'biocontainers/picrust2:2.5.2--pyhdfd78af_0' }"
 
     input:
     path(seq)

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:2022.11"
+    container "qiime2/core:2023.7"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

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:2022.11"
+    container "qiime2/core:2023.7"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

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:2022.11"
+    container "qiime2/core:2023.7"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

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:2022.11"
+    container "qiime2/core:2023.7"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

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:2022.11"
+    container "qiime2/core:2023.7"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

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:2022.11"
+    container "qiime2/core:2023.7"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

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:2022.11"
+    container "qiime2/core:2023.7"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

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:2022.11"
+    container "qiime2/core:2023.7"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

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:2022.11"
+    container "qiime2/core:2023.7"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

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:2022.11"
+    container "qiime2/core:2023.7"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {