diff --git a/conf/modules.config b/conf/modules.config
index 37798f8d..60e0629d 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -399,6 +399,14 @@ process {
         ]
     }
 
+    withName: MAKE_REPORT_BUNDLE {
+        publishDir = [
+            path: { "${params.outdir}/report" },
+            mode: params.publish_dir_mode,
+            pattern: '*.zip'
+        ]
+    }
+
     withName: CUSTOM_MATRIXFILTER {
         publishDir = [
             enabled: false
diff --git a/modules.json b/modules.json
index dcf9482f..0340f17b 100644
--- a/modules.json
+++ b/modules.json
@@ -67,7 +67,7 @@
                     },
                     "rmarkdownnotebook": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "git_sha": "4e640839b1076da7c2a2a4a8f160815e00eedfba",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/app": {
@@ -94,6 +94,11 @@
                         "branch": "master",
                         "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
                         "installed_by": ["modules"]
+                    },
+                    "zip": {
+                        "branch": "master",
+                        "git_sha": "363ab4f7ed481242f5b1d73f81ffe76cea33fdaf",
+                        "installed_by": ["modules"]
                     }
                 }
             },
diff --git a/modules/nf-core/rmarkdownnotebook/main.nf b/modules/nf-core/rmarkdownnotebook/main.nf
index 45ed550b..3eda8ee9 100644
--- a/modules/nf-core/rmarkdownnotebook/main.nf
+++ b/modules/nf-core/rmarkdownnotebook/main.nf
@@ -18,10 +18,11 @@ process RMARKDOWNNOTEBOOK {
     path input_files
 
     output:
-    tuple val(meta), path("*.html")           , emit: report
-    tuple val(meta), path ("artifacts/*")     , emit: artifacts, optional: true
-    tuple val(meta), path ("session_info.log"), emit: session_info
-    path  "versions.yml"                      , emit: versions
+    tuple val(meta), path("*.html")              , emit: report
+    tuple val(meta), path("*.parameterised.Rmd") , emit: parameterised_notebook, optional: true
+    tuple val(meta), path ("artifacts/*")        , emit: artifacts, optional: true
+    tuple val(meta), path ("session_info.log")   , emit: session_info
+    path  "versions.yml"                         , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -53,10 +54,53 @@ process RMARKDOWNNOTEBOOK {
         params_cmd = dump_params_yml(nb_params)
         render_cmd = """\
             params = yaml::read_yaml('.params.yml')
-            rmarkdown::render('${prefix}.Rmd', params=params, envir=new.env())
+
+            # Instead of rendering with params, produce a version of the R
+            # markdown with param definitions set, so the notebook itself can
+            # be reused
+            rmd_content <- readLines('${prefix}.Rmd')
+
+            # Extract YAML content between the first two '---'
+            start_idx <- which(rmd_content == "---")[1]
+            end_idx <- which(rmd_content == "---")[2]
+            rmd_yaml_content <- paste(rmd_content[(start_idx+1):(end_idx-1)], collapse = "\\n")
+            rmd_params <- yaml::yaml.load(rmd_yaml_content)
+
+            # Override the params
+            rmd_params[['params']] <- modifyList(rmd_params[['params']], params)
+
+            # Recursive function to add 'value' to list elements, except for top-level
+            add_value_recursively <- function(lst, is_top_level = FALSE) {
+                if (!is.list(lst)) {
+                    return(lst)
+                }
+
+                lst <- lapply(lst, add_value_recursively)
+                if (!is_top_level) {
+                    lst <- list(value = lst)
+                }
+                return(lst)
+            }
+
+            # Reformat nested lists under 'params' to have a 'value' key recursively
+            rmd_params[['params']] <- add_value_recursively(rmd_params[['params']], is_top_level = TRUE)
+
+            # Convert back to YAML string
+            updated_yaml_content <- as.character(yaml::as.yaml(rmd_params))
+
+            # Remove the old YAML content
+            rmd_content <- rmd_content[-((start_idx+1):(end_idx-1))]
+
+            # Insert the updated YAML content at the right position
+            rmd_content <- append(rmd_content, values = unlist(strsplit(updated_yaml_content, split = "\\n")), after = start_idx)
+
+            writeLines(rmd_content, '${prefix}.parameterised.Rmd')
+
+            # Render based on the updated file
+            rmarkdown::render('${prefix}.parameterised.Rmd', output_file='${prefix}.html', envir = new.env())
         """
     } else {
-        render_cmd = "rmarkdown::render('${prefix}.Rmd')"
+        render_cmd = "rmarkdown::render('${prefix}.Rmd', output_file='${prefix}.html')"
     }
 
     """
diff --git a/tower.yml b/tower.yml
index 098d132c..98dd2a5f 100644
--- a/tower.yml
+++ b/tower.yml
@@ -1,6 +1,8 @@
 reports:
   "**/report/*.html":
     display: "Final differential abundance report"
+ "**/report/*.zip":
+    display: "Report bundle (markdown + input files)"
   pipeline_info/**:
     display: "Pipeline run info"
   "**/plots/exploratory/**/html/*.html":
diff --git a/workflows/differentialabundance.nf b/workflows/differentialabundance.nf
index 5f2ed24a..72bccf88 100644
--- a/workflows/differentialabundance.nf
+++ b/workflows/differentialabundance.nf
@@ -127,6 +127,7 @@ include { AFFY_JUSTRMA as AFFY_JUSTRMA_RAW                  } from '../modules/n
 include { AFFY_JUSTRMA as AFFY_JUSTRMA_NORM                 } from '../modules/nf-core/affy/justrma/main'
 include { PROTEUS_READPROTEINGROUPS as PROTEUS              } from '../modules/nf-core/proteus/readproteingroups/main'
 include { GEOQUERY_GETGEO                                   } from '../modules/nf-core/geoquery/getgeo/main'
+include { ZIP as MAKE_REPORT_BUNDLE                         } from '../modules/nf-core/zip/main'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -584,6 +585,15 @@ workflow DIFFERENTIALABUNDANCE {
         ch_report_input_files
     )
 
+    // Make a report bundle comprising the markdown document and all necessary
+    // input files
+
+    MAKE_REPORT_BUNDLE(
+        RMARKDOWNNOTEBOOK.out.parameterised_notebook
+            .combine(ch_report_input_files)
+            .map{[it[0], it[1..-1]]}
+    )
+
 }
 
 /*