diff --git a/assets/email_template.html b/assets/email_template.html
index dc46d39ee..e4639cdb6 100644
--- a/assets/email_template.html
+++ b/assets/email_template.html
@@ -34,25 +34,6 @@ <h4 style="margin-top: 0; color: inherit">nf-core/rnaseq execution completed uns
         <p>The full error message was:</p>
         <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0">${errorReport}</pre>
       </div>
-      """ } else if(skip_sample_count > 0) { out << """
-      <div
-        style="
-          color: #856404;
-          background-color: #fff3cd;
-          border-color: #ffeeba;
-          padding: 15px;
-          margin-bottom: 20px;
-          border: 1px solid transparent;
-          border-radius: 4px;
-        "
-      >
-        <h4 style="margin-top: 0; color: inherit">nf-core/rnaseq execution completed with warnings!</h4>
-        <p>
-          The pipeline finished successfully, but samples were skipped. Please check warnings at the top of the MultiQC report.
-        </p>
-        <p></p>
-      </div>
-
       """ } else { out << """
       <div
         style="
diff --git a/assets/email_template.txt b/assets/email_template.txt
index 8789fd8ae..ea2df520d 100644
--- a/assets/email_template.txt
+++ b/assets/email_template.txt
@@ -17,13 +17,6 @@ The full error message was:
 
 ${errorReport}
 """
-} else if (skip_sample_count > 0) {
-    out << """##################################################
-## nf-core/rnaseq execution completed with warnings ##
-##################################################
-The pipeline finished successfully, but samples were skipped.
-Please check warnings at the top of the MultiQC report.
-"""
 } else {
     out << "## nf-core/rnaseq execution completed successfully! ##"
 }
diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
index aa0dd4ed7..d733670bb 100644
--- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
@@ -116,10 +116,16 @@ workflow PIPELINE_COMPLETION {
             id, status -> pass_strand_check[id] = status
         }
 
+    // We need to ensure that the multiqc_report is a value channel (DataflowVariable).
+    // Queue channels will not be available in the workflow.onComplete block.
+    def multiqc_reports = multiqc_report.toList()
+
     //
     // Completion email and summary
     //
     workflow.onComplete {
+        assert multiqc_reports instanceof groovyx.gpars.dataflow.DataflowVariable : "Expected a value channel (DataflowVariable) for multiqc_reports inside workflow.onComplete block."
+
         if (email || email_on_fail) {
             completionEmail(
                 summary_params,
@@ -128,7 +134,7 @@ workflow PIPELINE_COMPLETION {
                 plaintext_email,
                 outdir,
                 monochrome_logs,
-                multiqc_report.toList()
+                multiqc_reports.getVal(),
             )
         }
 
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 5cb7bafef..14978183b 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -248,32 +248,29 @@ def logColours(monochrome_logs=true) {
 //
 // Attach the multiqc report to email
 //
-def attachMultiqcReport(multiqc_report) {
-    def mqc_report = null
-    try {
-        if (workflow.success) {
-            mqc_report = multiqc_report.getVal()
-            if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
-                if (mqc_report.size() > 1) {
+def getSingleReport(multiqc_reports) {
+    switch (multiqc_reports) {
+        case Path:
+            return multiqc_reports
+        case List:
+            switch (multiqc_reports.size()) {
+                case 0:
+                    log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'")
+                    return null
+                case 1:
+                    return multiqc_reports.first()
+                default:
                     log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
-                }
-                mqc_report = mqc_report[0]
+                    return multiqc_reports.first()
             }
-        }
-    }
-    catch (Exception all) {
-        if (multiqc_report) {
-            log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email")
-        }
+        default:
+            return null
     }
-    return mqc_report
 }
-
 //
 // Construct and send completion email
 //
-def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) {
-
+def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_reports=[]) {
     // Set up the e-mail variables
     def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}"
     if (!workflow.success) {
@@ -320,7 +317,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     email_fields['summary']      = summary << misc_fields
 
     // On success try attach the multiqc report
-    def mqc_report = attachMultiqcReport(multiqc_report)
+    def mqc_report = getSingleReport(multiqc_reports)
 
     // Check if we are only sending emails on failure
     def email_address = email
@@ -351,7 +348,8 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     if (email_address) {
         try {
             if (plaintext_email) {
-new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')            }
+                new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')            
+            }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }