Oncomplete fix

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="

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! ##"
 }

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(),
             )
         }