diff --git a/conf/test_multi.config b/conf/test_multi.config
index ea3e2e85..543a0271 100644
--- a/conf/test_multi.config
+++ b/conf/test_multi.config
@@ -30,4 +30,7 @@ params {
     dada_ref_taxonomy = "rdp=18"
     skip_dada_addspecies = true
     input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/Samplesheet_multi.tsv"
+
+    skip_phyloseq = true
+    skip_tse = true
 }
diff --git a/conf/test_pacbio_its.config b/conf/test_pacbio_its.config
index 65350d17..22177901 100644
--- a/conf/test_pacbio_its.config
+++ b/conf/test_pacbio_its.config
@@ -37,4 +37,6 @@ params {
 
     // Prevent default taxonomic classification
     skip_dada_taxonomy = true
+
+    skip_phyloseq = true
 }
diff --git a/conf/test_reftaxcustom.config b/conf/test_reftaxcustom.config
index c87f1ab9..7ad52aa9 100644
--- a/conf/test_reftaxcustom.config
+++ b/conf/test_reftaxcustom.config
@@ -37,4 +37,6 @@ params {
 
     // Skip downstream analysis with QIIME2
     skip_qiime_downstream = true
+
+    skip_tse = true
 }
diff --git a/tests/pipeline/doubleprimers.nf.test b/tests/pipeline/doubleprimers.nf.test
index 2b81571c..0e305f28 100644
--- a/tests/pipeline/doubleprimers.nf.test
+++ b/tests/pipeline/doubleprimers.nf.test
@@ -32,6 +32,7 @@ nextflow_pipeline {
                 { assert snapshot(path("$outputDir/input/Samplesheet_double_primer.tsv")).match("input") },
                 { assert new File("$outputDir/qiime2/abundance_tables/feature-table.tsv").exists() },
                 { assert new File("$outputDir/phyloseq/kraken2_phyloseq.rds").exists() },
+                { assert new File("$outputDir/treesummarizedexperiment/kraken2_TreeSummarizedExperiment.rds").exists() },
                 { assert snapshot(path("$outputDir/kraken2/ASV_tax.greengenes.kraken2.classifiedreads.txt"),
                                 path("$outputDir/kraken2/ASV_tax.greengenes.kraken2.complete.tsv"),
                                 path("$outputDir/kraken2/ASV_tax.greengenes.kraken2.tsv")).match("kraken2") },
diff --git a/tests/pipeline/failed.nf.test b/tests/pipeline/failed.nf.test
index dd39b9b1..032635b4 100644
--- a/tests/pipeline/failed.nf.test
+++ b/tests/pipeline/failed.nf.test
@@ -29,7 +29,8 @@ nextflow_pipeline {
                 { assert new File("$outputDir/qiime2/diversity/alpha_diversity/shannon_vector/kruskal-wallis-pairwise-treatment1.csv").exists() },
                 { assert new File("$outputDir/qiime2/diversity/beta_diversity/bray_curtis_pcoa_results-PCoA/index.html").exists() },
                 { assert new File("$outputDir/summary_report/summary_report.html").exists() },
-                { assert new File("$outputDir/phyloseq/dada2_phyloseq.rds").exists() }
+                { assert new File("$outputDir/phyloseq/dada2_phyloseq.rds").exists() },
+                { assert new File("$outputDir/treesummarizedexperiment/dada2_TreeSummarizedExperiment.rds").exists() }
             )
         }
     }
diff --git a/tests/pipeline/iontorrent.nf.test b/tests/pipeline/iontorrent.nf.test
index 98d1618f..d14a831e 100644
--- a/tests/pipeline/iontorrent.nf.test
+++ b/tests/pipeline/iontorrent.nf.test
@@ -38,7 +38,8 @@ nextflow_pipeline {
                                 path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
                                 path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") },
                 { assert new File("$outputDir/summary_report/summary_report.html").exists() },
-                { assert new File("$outputDir/phyloseq/sintax_phyloseq.rds").exists() }
+                { assert new File("$outputDir/phyloseq/sintax_phyloseq.rds").exists() },
+                { assert new File("$outputDir/treesummarizedexperiment/sintax_TreeSummarizedExperiment.rds").exists() }
             )
         }
     }
diff --git a/tests/pipeline/multi.nf.test b/tests/pipeline/multi.nf.test
index 59dd21b5..10eef81c 100644
--- a/tests/pipeline/multi.nf.test
+++ b/tests/pipeline/multi.nf.test
@@ -64,8 +64,7 @@ nextflow_pipeline {
                 { assert new File("$outputDir/qiime2/representative_sequences/rep-seq.fasta").exists() },
                 { assert snapshot(path("$outputDir/qiime2/representative_sequences/descriptive_stats.tsv"),
                                 path("$outputDir/qiime2/representative_sequences/seven_number_summary.tsv")).match("qiime2") },
-                { assert new File("$outputDir/summary_report/summary_report.html").exists() },
-                { assert new File("$outputDir/phyloseq/dada2_phyloseq.rds").exists() }
+                { assert new File("$outputDir/summary_report/summary_report.html").exists() }
             )
         }
     }
diff --git a/tests/pipeline/pacbio_its.nf.test b/tests/pipeline/pacbio_its.nf.test
index e4092920..f1c811b7 100644
--- a/tests/pipeline/pacbio_its.nf.test
+++ b/tests/pipeline/pacbio_its.nf.test
@@ -50,7 +50,7 @@ nextflow_pipeline {
                 { assert new File("$outputDir/SBDI/annotation.tsv").exists() },
                 { assert new File("$outputDir/SBDI/asv-table.tsv").exists() },
                 { assert new File("$outputDir/summary_report/summary_report.html").exists() },
-                { assert new File("$outputDir/phyloseq/sintax_phyloseq.rds").exists() }
+                { assert new File("$outputDir/treesummarizedexperiment/sintax_TreeSummarizedExperiment.rds").exists() }
             )
         }
     }
diff --git a/tests/pipeline/pplace.nf.test b/tests/pipeline/pplace.nf.test
index 0c6f4f67..c1851020 100644
--- a/tests/pipeline/pplace.nf.test
+++ b/tests/pipeline/pplace.nf.test
@@ -58,7 +58,9 @@ nextflow_pipeline {
                                 path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") },
                 { assert new File("$outputDir/summary_report/summary_report.html").exists() },
                 { assert new File("$outputDir/phyloseq/qiime2_phyloseq.rds").exists() },
-                { assert new File("$outputDir/phyloseq/pplace_phyloseq.rds").exists() }
+                { assert new File("$outputDir/phyloseq/pplace_phyloseq.rds").exists() },
+                { assert new File("$outputDir/treesummarizedexperiment/qiime2_TreeSummarizedExperiment.rds").exists() },
+                { assert new File("$outputDir/treesummarizedexperiment/pplace_TreeSummarizedExperiment.rds").exists() }
             )
         }
     }
diff --git a/tests/pipeline/single.nf.test b/tests/pipeline/single.nf.test
index add750b9..68abd513 100644
--- a/tests/pipeline/single.nf.test
+++ b/tests/pipeline/single.nf.test
@@ -46,7 +46,8 @@ nextflow_pipeline {
                                 path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
                                 path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") },
                 { assert new File("$outputDir/summary_report/summary_report.html").exists() },
-                { assert new File("$outputDir/phyloseq/dada2_phyloseq.rds").exists() }
+                { assert new File("$outputDir/phyloseq/dada2_phyloseq.rds").exists() },
+                { assert new File("$outputDir/treesummarizedexperiment/dada2_TreeSummarizedExperiment.rds").exists() }
             )
         }
     }
diff --git a/tests/pipeline/sintax.nf.test b/tests/pipeline/sintax.nf.test
index 03490f18..78194221 100644
--- a/tests/pipeline/sintax.nf.test
+++ b/tests/pipeline/sintax.nf.test
@@ -67,7 +67,8 @@ nextflow_pipeline {
                 { assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
                                 path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") },
                 { assert new File("$outputDir/summary_report/summary_report.html").exists() },
-                { assert new File("$outputDir/phyloseq/sintax_phyloseq.rds").exists() }
+                { assert new File("$outputDir/phyloseq/sintax_phyloseq.rds").exists() },
+                { assert new File("$outputDir/treesummarizedexperiment/sintax_TreeSummarizedExperiment.rds").exists() }
             )
         }
     }
diff --git a/tests/pipeline/test.nf.test b/tests/pipeline/test.nf.test
index 2c215ad3..06b42216 100644
--- a/tests/pipeline/test.nf.test
+++ b/tests/pipeline/test.nf.test
@@ -102,6 +102,8 @@ nextflow_pipeline {
                 { assert new File("$outputDir/summary_report/summary_report.html").exists() },
                 { assert new File("$outputDir/phyloseq/dada2_phyloseq.rds").exists() },
                 { assert new File("$outputDir/phyloseq/qiime2_phyloseq.rds").exists() },
+                { assert new File("$outputDir/treesummarizedexperiment/dada2_TreeSummarizedExperiment.rds").exists() },
+                { assert new File("$outputDir/treesummarizedexperiment/qiime2_TreeSummarizedExperiment.rds").exists() },
                 { assert snapshot(path("$outputDir/vsearch_cluster/ASV_post_clustering_filtered.fna"),
                                 path("$outputDir/vsearch_cluster/ASV_post_clustering_filtered.stats.tsv"),
                                 path("$outputDir/vsearch_cluster/ASV_post_clustering_filtered.table.tsv")).match("vsearch_cluster") }