From e1f07d5566aed6371638307e72f1c9e6c20c7ca5 Mon Sep 17 00:00:00 2001
From: Rob Syme <rob.syme@gmail.com>
Date: Mon, 2 Dec 2024 16:15:01 -0500
Subject: [PATCH] Revert changes to nf-core module

---
 .../nf-core/utils_nfcore_pipeline/main.nf     | 40 +++++++++----------
 1 file changed, 20 insertions(+), 20 deletions(-)

diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index f050f67072..5cb7bafef3 100644
--- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -246,26 +246,27 @@ def logColours(monochrome_logs=true) {
 }
 
 //
-// Return a single report from an object that may be a Path or List
-//
-def getSingleReport(multiqc_reports) {
-    switch (multiqc_reports) {
-        case Path:
-            return multiqc_reports
-        case List:
-            switch (multiqc_reports.size()) {
-                case 0:
-                    log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'")
-                    return null
-                case 1:
-                    return multiqc_reports.first()
-                default:
+// Attach the multiqc report to email
+//
+def attachMultiqcReport(multiqc_report) {
+    def mqc_report = null
+    try {
+        if (workflow.success) {
+            mqc_report = multiqc_report.getVal()
+            if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
+                if (mqc_report.size() > 1) {
                     log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
-                    return multiqc_reports.first()
+                }
+                mqc_report = mqc_report[0]
             }
-        default:
-            return null
+        }
+    }
+    catch (Exception all) {
+        if (multiqc_report) {
+            log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email")
+        }
     }
+    return mqc_report
 }
 
 //
@@ -319,7 +320,7 @@ 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 = getSingleReport(multiqc_report)
+    def mqc_report = attachMultiqcReport(multiqc_report)
 
     // Check if we are only sending emails on failure
     def email_address = email
@@ -350,8 +351,7 @@ 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 }