Ensure that the onComplete block doesn't hang.

nf-core · Nov 29, 2024 · 4773e58 · 4773e58
1 parent c4fb145
commit 4773e58
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Showing 2 changed files with 26 additions and 22 deletions.
diff --git 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