From 8a2320d34515e3a37209f4b4a43752acfa2fe611 Mon Sep 17 00:00:00 2001
From: Florian De Temmerman <florian.detemmerman@pixelgen.com>
Date: Mon, 16 Oct 2023 16:23:40 +0200
Subject: [PATCH] fix remote outdir in NfCoreTemplate.groovy

See: https://github.com/nf-core/tools/pull/2465
---
 lib/NfcoreTemplate.groovy | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
index 0498726a..66ad49d4 100755
--- a/lib/NfcoreTemplate.groovy
+++ b/lib/NfcoreTemplate.groovy
@@ -156,14 +156,16 @@ class NfcoreTemplate {
         }
 
         // Write summary e-mail HTML to a file
-        def output_d = new File("${params.outdir}/pipeline_info/")
-        if (!output_d.exists()) {
-            output_d.mkdirs()
-        }
-        def output_hf = new File(output_d, "pipeline_report.html")
+        def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
         output_hf.withWriter { w -> w << email_html }
-        def output_tf = new File(output_d, "pipeline_report.txt")
+        FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html");
+        output_hf.delete()
+
+        // Write summary e-mail TXT to a file
+        def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
         output_tf.withWriter { w -> w << email_txt }
+        FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt");
+        output_tf.delete()
     }
 
     //
@@ -234,8 +236,7 @@ class NfcoreTemplate {
         def jsonStr    = JsonOutput.toJson(params)
         temp_pf.text   = JsonOutput.prettyPrint(jsonStr)
 
-        def destination = "${params.outdir}/pipeline_info/params_${timestamp}.json"
-        FilesEx.copyTo(temp_pf.toPath(), destination)
+        FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json")
         temp_pf.delete()
     }