diff --git a/CHANGELOG.md b/CHANGELOG.md
index dd44453b..c41dd5ec 100644
--- 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`
 
+- [[#266](https://github.com/nf-core/differentialabundance/pull/266)] - Fix logging by specifying assays to log ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 - [[#259](https://github.com/nf-core/differentialabundance/pull/259)] - Bump gtf2featureannotation to fix GTF handling error ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 - [[#257](https://github.com/nf-core/differentialabundance/pull/257)] - Added maxquant profile to nextflow.config to make it available ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#254](https://github.com/nf-core/differentialabundance/pull/254)] - Some parameter changes, added qbic credits ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd
index fa8787f1..7bf41c12 100644
--- a/assets/differentialabundance_report.Rmd
+++ b/assets/differentialabundance_report.Rmd
@@ -38,7 +38,7 @@ params:
     features_metadata_cols: NULL
     features_gtf_feature_type: NULL
     features_gtf_table_first_field: NULL
-    features_log2_assays: NULL
+    exploratory_log2_assays: NULL
     raw_matrix: null                                            # e.g. 0_salmon.merged.gene_counts_length_scaled.tsv
     normalised_matrix: null
     variance_stabilised_matrix: null                            # e.g. test_files/3_treatment-WT-P23H.vst.tsv
@@ -310,11 +310,12 @@ assay_data <- lapply(assay_files, function(x) {
     mat
 })
 
-if (!is.null(params$features_log2_assays)) {
+log2_assays <- params$exploratory_log2_assays
+if (!is.null(log2_assays)) {
     # Remove brackets from assay list. TODO: remove if this is added to cond_log2_transform_assays
-    params$features_log2_assays <- gsub('\\]$', '', gsub('^\\[', '', params$features_log2_assays))
+    log2_assays <- gsub('\\]$', '', gsub('^\\[', '', log2_assays))
 }
-assay_data <- cond_log2_transform_assays(assay_data, params$features_log2_assays)
+assay_data <- cond_log2_transform_assays(assay_data, log2_assays, prettify_names = FALSE)
 
 # Now we can rename the observations rows using the title field
 rownames(observations) <- observations[[observations_name_col]]
diff --git a/conf/affy.config b/conf/affy.config
index 7d953d3b..d0ceb7a3 100644
--- a/conf/affy.config
+++ b/conf/affy.config
@@ -27,6 +27,7 @@ params {
     // Exploratory
     exploratory_assay_names = 'raw,normalised'
     exploratory_final_assay = 'normalised'
+    exploratory_log2_assays = null
 
     // Differential options
     differential_file_suffix         = ".limma.results.tsv"
diff --git a/conf/maxquant.config b/conf/maxquant.config
index 57caf2d4..8adf03c8 100644
--- a/conf/maxquant.config
+++ b/conf/maxquant.config
@@ -28,6 +28,7 @@ params {
     // Exploratory
     exploratory_assay_names = "raw,normalised"
     exploratory_final_assay = "normalised"
+    exploratory_log2_assays = null
 
     // Differential options
     differential_file_suffix         = ".limma.results.tsv"
diff --git a/conf/modules.config b/conf/modules.config
index c5eee153..9313457d 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -375,7 +375,7 @@ process {
             "--final_assay \"${params.exploratory_final_assay}\"",
             "--outlier_mad_threshold ${params.exploratory_mad_threshold}",
             "--palette_name \"${params.exploratory_palette_name}\"",
-            ( (params.study_type == 'maxquant') ? "--log2_assays ''" : (((params.features_log2_assays == null) ? '' : "--log2_assays \"$params.features_log2_assays\"".replace('[', '').replace(']', ''))) )
+            ( (params.study_type == 'maxquant') ? "--log2_assays ''" : (((params.exploratory_log2_assays == null) ? '' : "--log2_assays \"$params.exploratory_log2_assays\"".replace('[', '').replace(']', ''))) )
         ].join(' ').trim() }
     }
 
@@ -428,8 +428,8 @@ process {
     }
 
     withName: RMARKDOWNNOTEBOOK {
-        conda = "bioconda::r-shinyngs=1.8.4"
-        container = { "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.4--r43hdfd78af_0' : 'biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0' }" }
+        conda = "bioconda::r-shinyngs=1.8.8"
+        container = { "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.8--r43hdfd78af_0' : 'biocontainers/r-shinyngs:1.8.8--r43hdfd78af_0' }" }
         publishDir = [
             [
                 path: { "${params.outdir}/report" },
diff --git a/conf/rnaseq.config b/conf/rnaseq.config
index 10427bf1..c79d4828 100644
--- a/conf/rnaseq.config
+++ b/conf/rnaseq.config
@@ -27,6 +27,7 @@ params {
     // Exploratory
     exploratory_assay_names = "raw,normalised,variance_stabilised"
     exploratory_final_assay = "variance_stabilised"
+    exploratory_log2_assays = 'raw,normalised'
 
     // Differential options
     differential_file_suffix         = ".deseq2.results.tsv"
diff --git a/conf/soft.config b/conf/soft.config
index 5109b25d..832ebc17 100644
--- a/conf/soft.config
+++ b/conf/soft.config
@@ -33,6 +33,7 @@ params {
     // Exploratory
     exploratory_assay_names = 'normalised'
     exploratory_final_assay = 'normalised'
+    exploratory_log2_assays = null
 
     // Differential options
     differential_file_suffix         = ".limma.results.tsv"
diff --git a/modules.json b/modules.json
index c313b064..6362693e 100644
--- a/modules.json
+++ b/modules.json
@@ -72,22 +72,22 @@
                     },
                     "shinyngs/app": {
                         "branch": "master",
-                        "git_sha": "d2d6072ae4c3a9d394dfe773bb0751f34df7a896",
+                        "git_sha": "85519fe9deccf2c5f7ff1f3b5d3494c61a794643",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/staticdifferential": {
                         "branch": "master",
-                        "git_sha": "d2d6072ae4c3a9d394dfe773bb0751f34df7a896",
+                        "git_sha": "85519fe9deccf2c5f7ff1f3b5d3494c61a794643",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/staticexploratory": {
                         "branch": "master",
-                        "git_sha": "d2d6072ae4c3a9d394dfe773bb0751f34df7a896",
+                        "git_sha": "85519fe9deccf2c5f7ff1f3b5d3494c61a794643",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/validatefomcomponents": {
                         "branch": "master",
-                        "git_sha": "d2d6072ae4c3a9d394dfe773bb0751f34df7a896",
+                        "git_sha": "85519fe9deccf2c5f7ff1f3b5d3494c61a794643",
                         "installed_by": ["modules"]
                     },
                     "untar": {
@@ -111,7 +111,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
diff --git a/modules/nf-core/shinyngs/app/environment.yml b/modules/nf-core/shinyngs/app/environment.yml
index 9d051f47..0e6de401 100644
--- a/modules/nf-core/shinyngs/app/environment.yml
+++ b/modules/nf-core/shinyngs/app/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::r-shinyngs=1.8.5
+  - bioconda::r-shinyngs=1.8.8
diff --git a/modules/nf-core/shinyngs/app/main.nf b/modules/nf-core/shinyngs/app/main.nf
index 3a023aa1..ef05a863 100644
--- a/modules/nf-core/shinyngs/app/main.nf
+++ b/modules/nf-core/shinyngs/app/main.nf
@@ -15,8 +15,8 @@ process SHINYNGS_APP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.5--r43hdfd78af_0' :
-        'biocontainers/r-shinyngs:1.8.5--r43hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.8--r43hdfd78af_0' :
+        'biocontainers/r-shinyngs:1.8.8--r43hdfd78af_0' }"
 
     input:
     tuple val(meta), path(sample), path(feature_meta), path(assay_files)    // Experiment-level info
@@ -49,8 +49,23 @@ process SHINYNGS_APP {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
         r-shinyngs: \$(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: meta.id
+
+    """
+    mkdir -p $prefix
+    touch ${prefix}/data.rds
+    touch ${prefix}/app.R
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r-shinyngs: \$(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
+    END_VERSIONS
+    """
+
 }
diff --git a/modules/nf-core/shinyngs/app/tests/main.nf.test b/modules/nf-core/shinyngs/app/tests/main.nf.test
new file mode 100644
index 00000000..39d6e27e
--- /dev/null
+++ b/modules/nf-core/shinyngs/app/tests/main.nf.test
@@ -0,0 +1,133 @@
+nextflow_process {
+
+    name "Test Process SHINYNGS_APP"
+    script "../main.nf"
+    process "SHINYNGS_APP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "shinyngs"
+    tag "shinyngs/app"
+
+    test("mouse - multi matrix") {
+
+        config './nextflow.config'
+
+        when {
+            process {
+                """
+                expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/'
+
+                expression_sample_sheet = file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true)
+                expression_feature_meta = file(expression_test_data_dir + 'SRP254919.gene_meta.tsv', checkIfExists: true)
+                raw_expression_matrix_file = file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
+                expression_contrasts = file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)
+                expression_differential = file(expression_test_data_dir + 'SRP254919.salmon.merged.deseq2.results.tsv', checkIfExists: true)
+
+                // Copy some inputs for testing the multi-matrix functionality
+                raw_expression_matrix_file.copyTo('normalised.tsv')
+                normalised_expression_matrix_file = file('normalised.tsv') 
+                expression_differential.copyTo('second_contrast_stats.tsv')
+                second_contrast_stats = file('second_contrast_stats.tsv')
+
+                contrast_stats_assay = Channel.value(1)
+
+                input[0] = [ [ "id":"SRP254919" ], expression_sample_sheet,  expression_feature_meta, [ raw_expression_matrix_file, normalised_expression_matrix_file ] ]
+                input[1] = [ [ "id":"SRP254919" ], expression_contrasts, [ expression_differential, second_contrast_stats  ] ]
+                input[2] = contrast_stats_assay 
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.app[0][1]).name,
+                    process.out.app[0][2],
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+    
+    test("mouse - single matrix") {
+
+        config './nextflow.config'
+        
+        when {
+            process {
+                """
+                expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/'
+
+                expression_sample_sheet = file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true)
+                expression_feature_meta = file(expression_test_data_dir + 'SRP254919.gene_meta.tsv', checkIfExists: true)
+                raw_expression_matrix_file = file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
+                expression_contrasts = file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)
+                expression_differential = file(expression_test_data_dir + 'SRP254919.salmon.merged.deseq2.results.tsv', checkIfExists: true)
+
+                // Copy some inputs for testing the multi-matrix functionality
+                expression_differential.copyTo('second_contrast_stats.tsv')
+                second_contrast_stats = file('second_contrast_stats.tsv')
+
+                contrast_stats_assay = Channel.value(1)
+
+                input[0] = [ [ "id":"SRP254919" ], expression_sample_sheet,  expression_feature_meta, [ raw_expression_matrix_file ] ]
+                input[1] = [ [ "id":"SRP254919" ], expression_contrasts, [ expression_differential, second_contrast_stats  ] ]
+                input[2] = contrast_stats_assay 
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.app[0][1]).name,
+                    process.out.app[0][2],
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+    
+    test("mouse - stub") {
+
+        options "-stub"
+        
+        when {
+            process {
+                """
+                expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/'
+
+                expression_sample_sheet = file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true)
+                expression_feature_meta = file(expression_test_data_dir + 'SRP254919.gene_meta.tsv', checkIfExists: true)
+                raw_expression_matrix_file = file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
+                expression_contrasts = file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)
+                expression_differential = file(expression_test_data_dir + 'SRP254919.salmon.merged.deseq2.results.tsv', checkIfExists: true)
+
+                // Copy some inputs for testing the multi-matrix functionality
+                expression_differential.copyTo('second_contrast_stats.tsv')
+                second_contrast_stats = file('second_contrast_stats.tsv')
+
+                contrast_stats_assay = Channel.value(1)
+
+                input[0] = [ [ "id":"SRP254919" ], expression_sample_sheet,  expression_feature_meta, [ raw_expression_matrix_file ] ]
+                input[1] = [ [ "id":"SRP254919" ], expression_contrasts, [ expression_differential, second_contrast_stats  ] ]
+                input[2] = contrast_stats_assay 
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.app[0][1]).name,
+                    process.out.app[0][2],
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/shinyngs/app/tests/main.nf.test.snap b/modules/nf-core/shinyngs/app/tests/main.nf.test.snap
new file mode 100644
index 00000000..f87c17d7
--- /dev/null
+++ b/modules/nf-core/shinyngs/app/tests/main.nf.test.snap
@@ -0,0 +1,44 @@
+{
+    "mouse - stub": {
+        "content": [
+            "data.rds",
+            "app.R:md5,d41d8cd98f00b204e9800998ecf8427e",
+            [
+                "versions.yml:md5,9a3135ae8ff362a9671b280dcc5781da"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-03T08:47:11.758494"
+    },
+    "mouse - multi matrix": {
+        "content": [
+            "data.rds",
+            "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a",
+            [
+                "versions.yml:md5,9a3135ae8ff362a9671b280dcc5781da"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-03T08:46:37.144273"
+    },
+    "mouse - single matrix": {
+        "content": [
+            "data.rds",
+            "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a",
+            [
+                "versions.yml:md5,9a3135ae8ff362a9671b280dcc5781da"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-03T08:46:57.227288"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/shinyngs/app/tests/nextflow.config b/modules/nf-core/shinyngs/app/tests/nextflow.config
new file mode 100644
index 00000000..b5fffed1
--- /dev/null
+++ b/modules/nf-core/shinyngs/app/tests/nextflow.config
@@ -0,0 +1,14 @@
+process {
+    //withName: test_shinyngs_app:SHINYNGS_APP {
+    //    secret 'SHINYAPPS_TOKEN'                                                  
+    //    secret 'SHINYAPPS_SECRET'  
+    //}
+    withName: test_shinyngs_app:SHINYNGS_APP {
+        ext.prefix = { "${meta.id}_test" }
+        ext.args = { "--contrast_stats_assay 1" }
+    }
+    withName: test_shinyngs_app_multi_matrix:SHINYNGS_APP {
+        ext.prefix = { "${meta.id}_test" }
+        ext.args = { "--assay-names raw,normalised --contrast_stats_assay 2" }
+    }
+}
diff --git a/modules/nf-core/shinyngs/app/tests/tags.yml b/modules/nf-core/shinyngs/app/tests/tags.yml
new file mode 100644
index 00000000..07331846
--- /dev/null
+++ b/modules/nf-core/shinyngs/app/tests/tags.yml
@@ -0,0 +1,2 @@
+shinyngs/app:
+  - "modules/nf-core/shinyngs/app/**"
diff --git a/modules/nf-core/shinyngs/staticdifferential/environment.yml b/modules/nf-core/shinyngs/staticdifferential/environment.yml
index 65ef5971..bec57084 100644
--- a/modules/nf-core/shinyngs/staticdifferential/environment.yml
+++ b/modules/nf-core/shinyngs/staticdifferential/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::r-shinyngs=1.8.5
+  - bioconda::r-shinyngs=1.8.8
diff --git a/modules/nf-core/shinyngs/staticdifferential/main.nf b/modules/nf-core/shinyngs/staticdifferential/main.nf
index 823eadc0..c61ccb4a 100644
--- a/modules/nf-core/shinyngs/staticdifferential/main.nf
+++ b/modules/nf-core/shinyngs/staticdifferential/main.nf
@@ -4,8 +4,8 @@ process SHINYNGS_STATICDIFFERENTIAL {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.5--r43hdfd78af_0' :
-        'biocontainers/r-shinyngs:1.8.5--r43hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.8--r43hdfd78af_0' :
+        'biocontainers/r-shinyngs:1.8.8--r43hdfd78af_0' }"
 
     input:
     tuple val(meta), path(differential_result)                              // Differential info: contrast and differential stats
diff --git a/modules/nf-core/shinyngs/staticexploratory/environment.yml b/modules/nf-core/shinyngs/staticexploratory/environment.yml
index 8fbe76e2..1c923f1b 100644
--- a/modules/nf-core/shinyngs/staticexploratory/environment.yml
+++ b/modules/nf-core/shinyngs/staticexploratory/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::r-shinyngs=1.8.5
+  - bioconda::r-shinyngs=1.8.8
diff --git a/modules/nf-core/shinyngs/staticexploratory/main.nf b/modules/nf-core/shinyngs/staticexploratory/main.nf
index fbbb26c3..1a3104b3 100644
--- a/modules/nf-core/shinyngs/staticexploratory/main.nf
+++ b/modules/nf-core/shinyngs/staticexploratory/main.nf
@@ -4,8 +4,8 @@ process SHINYNGS_STATICEXPLORATORY {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.5--r43hdfd78af_0' :
-        'biocontainers/r-shinyngs:1.8.5--r43hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.8--r43hdfd78af_0' :
+        'biocontainers/r-shinyngs:1.8.8--r43hdfd78af_0' }"
 
     input:
     tuple val(meta), path(sample), path(feature_meta), path(assay_files)
@@ -43,7 +43,29 @@ process SHINYNGS_STATICEXPLORATORY {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
+        r-shinyngs: \$(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: meta.id
+    """
+    mkdir -p ${prefix}/png ${prefix}/html
+    touch ${prefix}/png/boxplot.png
+    touch ${prefix}/html/boxplot.html
+    touch ${prefix}/png/density.png
+    touch ${prefix}/html/density.html
+    touch ${prefix}/png/pca2d.png
+    touch ${prefix}/html/pca3d.html
+    touch ${prefix}/png/pca3d.png
+    touch ${prefix}/html/pca2d.html
+    touch ${prefix}/png/mad_correlation.png
+    touch ${prefix}/html/mad_correlation.html
+    touch ${prefix}/png/sample_dendrogram.png
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
         r-shinyngs: \$(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
     END_VERSIONS
     """
diff --git a/modules/nf-core/shinyngs/staticexploratory/tests/main.nf.test b/modules/nf-core/shinyngs/staticexploratory/tests/main.nf.test
new file mode 100644
index 00000000..3338aba1
--- /dev/null
+++ b/modules/nf-core/shinyngs/staticexploratory/tests/main.nf.test
@@ -0,0 +1,154 @@
+nextflow_process {
+
+    name "Test Process SHINYNGS_STATICEXPLORATORY"
+    script "../main.nf"
+    process "SHINYNGS_STATICEXPLORATORY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "shinyngs"
+    tag "shinyngs/staticexploratory"
+
+    test("mouse - defaults") {
+
+        when {
+            process {
+                """
+                expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/'
+
+                expression_sample_sheet = file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true)
+                expression_feature_meta = file(expression_test_data_dir + 'SRP254919.gene_meta.tsv', checkIfExists: true)
+                expression_matrix_file = file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
+                
+                input[0] = [ [ "id":"treatment" ], expression_sample_sheet, expression_feature_meta, [ expression_matrix_file ] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.boxplots_png[0][1]).name,
+                    file(process.out.densities_png[0][1]).name,
+                    file(process.out.mad_png[0][1]).name,
+                    file(process.out.pca2d_png[0][1]).name,
+                    file(process.out.pca3d_png[0][1]).name,
+                    file(process.out.dendro[0][1]).name,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+    
+    test("mouse - defaults - stub") {
+        
+        options "-stub"
+
+        when {
+            process {
+                """
+                expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/'
+
+                expression_sample_sheet = file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true)
+                expression_feature_meta = file(expression_test_data_dir + 'SRP254919.gene_meta.tsv', checkIfExists: true)
+                expression_matrix_file = file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
+                
+                input[0] = [ [ "id":"treatment" ], expression_sample_sheet, expression_feature_meta, [ expression_matrix_file ] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.boxplots_png[0][1]).name,
+                    file(process.out.densities_png[0][1]).name,
+                    file(process.out.mad_png[0][1]).name,
+                    file(process.out.pca2d_png[0][1]).name,
+                    file(process.out.pca3d_png[0][1]).name,
+                    file(process.out.dendro[0][1]).name,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("mouse - specify log") {
+
+        config './nextflow_specify_log.conf'
+
+        when {
+            process {
+                """
+                expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/'
+
+                expression_sample_sheet = file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true)
+                expression_feature_meta = file(expression_test_data_dir + 'SRP254919.gene_meta.tsv', checkIfExists: true)
+                expression_matrix_file = file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
+                
+                input[0] = [ [ "id":"treatment" ], expression_sample_sheet, expression_feature_meta, [ expression_matrix_file ] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.boxplots_png[0][1]).name,
+                    file(process.out.densities_png[0][1]).name,
+                    file(process.out.mad_png[0][1]).name,
+                    file(process.out.pca2d_png[0][1]).name,
+                    file(process.out.pca3d_png[0][1]).name,
+                    file(process.out.dendro[0][1]).name,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+    
+    test("mouse - html") {
+
+        config './nextflow_html.conf'
+
+        when {
+            process {
+                """
+                expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/'
+
+                expression_sample_sheet = file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true)
+                expression_feature_meta = file(expression_test_data_dir + 'SRP254919.gene_meta.tsv', checkIfExists: true)
+                expression_matrix_file = file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
+                
+                input[0] = [ [ "id":"treatment" ], expression_sample_sheet, expression_feature_meta, [ expression_matrix_file ] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.boxplots_png[0][1]).name,
+                    file(process.out.densities_png[0][1]).name,
+                    file(process.out.mad_png[0][1]).name,
+                    file(process.out.pca2d_png[0][1]).name,
+                    file(process.out.pca3d_png[0][1]).name,
+                    file(process.out.dendro[0][1]).name,
+                    path(process.out.boxplots_html[0][1]).readLines().contains('ENSMUSG00000027456","Gm37080'),
+                    path(process.out.densities_html[0][1]).readLines().contains('-1.4916353753463203,-1.3078530974016225,-1.1240708194569247,-0.94028854151222707'),
+                    path(process.out.mad_html[0][1]).readLines().contains('0,-0.74295280067699376,0.67449075947659531,-0.6744907594765952'),
+                    path(process.out.pca2d_html[0][1]).readLines().contains('SRX8042381","SRX8042382'),
+                    path(process.out.pca3d_html[0][1]).readLines().contains('SRX8042381","SRX8042382'),
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/shinyngs/staticexploratory/tests/main.nf.test.snap b/modules/nf-core/shinyngs/staticexploratory/tests/main.nf.test.snap
new file mode 100644
index 00000000..b95d031c
--- /dev/null
+++ b/modules/nf-core/shinyngs/staticexploratory/tests/main.nf.test.snap
@@ -0,0 +1,79 @@
+{
+    "mouse - defaults - stub": {
+        "content": [
+            "boxplot.png",
+            "density.png",
+            "mad_correlation.png",
+            "pca2d.png",
+            "pca3d.png",
+            "sample_dendrogram.png",
+            [
+                "versions.yml:md5,526fbe61b95ad3a722d7470ca1874ca3"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-03T08:48:20.908769"
+    },
+    "mouse - defaults": {
+        "content": [
+            "boxplot.png",
+            "density.png",
+            "mad_correlation.png",
+            "pca2d.png",
+            "pca3d.png",
+            "sample_dendrogram.png",
+            [
+                "versions.yml:md5,526fbe61b95ad3a722d7470ca1874ca3"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-03T08:48:06.589763"
+    },
+    "mouse - specify log": {
+        "content": [
+            "boxplot.png",
+            "density.png",
+            "mad_correlation.png",
+            "pca2d.png",
+            "pca3d.png",
+            "sample_dendrogram.png",
+            [
+                "versions.yml:md5,526fbe61b95ad3a722d7470ca1874ca3"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-03T08:48:41.352789"
+    },
+    "mouse - html": {
+        "content": [
+            "boxplot.png",
+            "density.png",
+            "mad_correlation.png",
+            "pca2d.png",
+            "pca3d.png",
+            "sample_dendrogram.png",
+            false,
+            false,
+            false,
+            false,
+            false,
+            [
+                "versions.yml:md5,526fbe61b95ad3a722d7470ca1874ca3"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-03T08:49:04.969108"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/shinyngs/staticexploratory/tests/nextflow.config b/modules/nf-core/shinyngs/staticexploratory/tests/nextflow.config
new file mode 100644
index 00000000..399ac590
--- /dev/null
+++ b/modules/nf-core/shinyngs/staticexploratory/tests/nextflow.config
@@ -0,0 +1,8 @@
+process {
+    withName: 'test_shinyngs_staticexploratory_specify_log:SHINYNGS_STATICEXPLORATORY' {
+        ext.args = { "--log2_assays '1'" }
+    }
+    withName: 'test_shinyngs_staticexploratory_html:SHINYNGS_STATICEXPLORATORY' {
+        ext.args = { "--write_html" }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/shinyngs/staticexploratory/tests/nextflow_html.conf b/modules/nf-core/shinyngs/staticexploratory/tests/nextflow_html.conf
new file mode 100644
index 00000000..b7a293a4
--- /dev/null
+++ b/modules/nf-core/shinyngs/staticexploratory/tests/nextflow_html.conf
@@ -0,0 +1,5 @@
+process {
+    withName: 'SHINYNGS_STATICEXPLORATORY' {
+        ext.args = { "--write_html" }
+    }
+}
diff --git a/modules/nf-core/shinyngs/staticexploratory/tests/nextflow_specify_log.conf b/modules/nf-core/shinyngs/staticexploratory/tests/nextflow_specify_log.conf
new file mode 100644
index 00000000..0872df66
--- /dev/null
+++ b/modules/nf-core/shinyngs/staticexploratory/tests/nextflow_specify_log.conf
@@ -0,0 +1,5 @@
+process {
+    withName: 'SHINYNGS_STATICEXPLORATORY' {
+        ext.args = { "--log2_assays '1'" }
+    }
+}
diff --git a/modules/nf-core/shinyngs/staticexploratory/tests/tags.yml b/modules/nf-core/shinyngs/staticexploratory/tests/tags.yml
new file mode 100644
index 00000000..8e507165
--- /dev/null
+++ b/modules/nf-core/shinyngs/staticexploratory/tests/tags.yml
@@ -0,0 +1,2 @@
+shinyngs/staticexploratory:
+  - "modules/nf-core/shinyngs/staticexploratory/**"
diff --git a/modules/nf-core/shinyngs/validatefomcomponents/environment.yml b/modules/nf-core/shinyngs/validatefomcomponents/environment.yml
index 9fd7dfd8..4f3067bc 100644
--- a/modules/nf-core/shinyngs/validatefomcomponents/environment.yml
+++ b/modules/nf-core/shinyngs/validatefomcomponents/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::r-shinyngs=1.8.5
+  - bioconda::r-shinyngs=1.8.8
diff --git a/modules/nf-core/shinyngs/validatefomcomponents/main.nf b/modules/nf-core/shinyngs/validatefomcomponents/main.nf
index 88a6153a..fad3948a 100644
--- a/modules/nf-core/shinyngs/validatefomcomponents/main.nf
+++ b/modules/nf-core/shinyngs/validatefomcomponents/main.nf
@@ -4,8 +4,8 @@ process SHINYNGS_VALIDATEFOMCOMPONENTS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.5--r43hdfd78af_0' :
-        'biocontainers/r-shinyngs:1.8.5--r43hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.8--r43hdfd78af_0' :
+        'biocontainers/r-shinyngs:1.8.8--r43hdfd78af_0' }"
 
     input:
     tuple val(meta),  path(sample), path(assay_files)
diff --git a/nextflow.config b/nextflow.config
index abb083f8..6390c9bf 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -44,7 +44,6 @@ params {
     features_id_col             = 'gene_id'
     features_name_col           = 'gene_name'
     features_metadata_cols      = 'gene_id,gene_name,gene_biotype'
-    features_log2_assays        = null
 
     // GTF parsing options
     features_gtf_feature_type	    = 'transcript'
@@ -86,6 +85,7 @@ params {
     exploratory_mad_threshold      = -5
     exploratory_assay_names        = "raw,normalised,variance_stabilised"
     exploratory_final_assay        = "variance_stabilised"
+    exploratory_log2_assays        = 'raw,normalised'
     exploratory_palette_name       = 'Set1'
 
     // Differential options
diff --git a/nextflow_schema.json b/nextflow_schema.json
index f131c166..7e329647 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -190,11 +190,6 @@
                     "default": "gene_id",
                     "description": "Where a GTF file is supplied, which field should go first in the converted output table",
                     "fa_icon": "fas fa-fast-backward"
-                },
-                "features_log2_assays": {
-                    "type": "string",
-                    "description": "Of which assays to compute the log2. Not necessary for maxquant data as this is controlled by the pipeline.",
-                    "help_text": "Either comma-separated of assay positions, e.g. '[1,2,3]', or empty list '[]' to not log any assay. If not set, will guess which assays need to be logged (those with a maximum > 20)."
                 }
             },
             "required": ["features_id_col", "features_name_col", "features_type"],
@@ -403,6 +398,11 @@
                     "description": "Specifies final assay to be used for exploratory analysis, platform-specific",
                     "fa_icon": "fas fa-sort-down"
                 },
+                "exploratory_log2_assays": {
+                    "type": "string",
+                    "description": "Of which assays to compute the log2 during exploratory analysis. Not necessary for maxquant data as this is controlled by the pipeline.",
+                    "help_text": "Either comma-separated of assay positions, e.g. '[1,2,3]', or empty list '[]' to not log any assay. If not set, will guess which assays need to be logged (those with a maximum > 20)."
+                },
                 "exploratory_palette_name": {
                     "type": "string",
                     "default": "Set1",
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index a8b55d6f..14558c39 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -65,9 +65,15 @@ def checkProfileProvided(nextflow_cli_args) {
 // Citation string for pipeline
 //
 def workflowCitation() {
+    def temp_doi_ref = ""
+    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+    // Using a loop to handle multiple DOIs
+    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+    // Removing ` ` since the manifest.doi is a string and not a proper list
+    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
     return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
         "* The pipeline\n" +
-        "  ${workflow.manifest.doi}\n\n" +
+        temp_doi_ref + "\n" +
         "* The nf-core framework\n" +
         "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
         "* Software dependencies\n" +