From 27ff768e25b07d4cb92163392a6db6b6cda75da8 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sat, 18 May 2024 16:52:01 +0200
Subject: [PATCH] Remove completion handler + add emits

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 main.nf                 | 6 ------
 modules/fastqc/main.nf  | 2 +-
 modules/multiqc/main.nf | 2 +-
 3 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/main.nf b/main.nf
index 77d2d70..0b72c92 100755
--- a/main.nf
+++ b/main.nf
@@ -56,9 +56,3 @@ workflow {
   MULTIQC( RNASEQ.out, params.multiqc )
 }
 
-/* 
- * completion handler
- */
-workflow.onComplete {
-	log.info ( workflow.success ? "\nDone! Open the following report in your browser --> $params.outdir/multiqc_report.html\n" : "Oops .. something went wrong" )
-}
diff --git a/modules/fastqc/main.nf b/modules/fastqc/main.nf
index cd58cbb..b9009cd 100644
--- a/modules/fastqc/main.nf
+++ b/modules/fastqc/main.nf
@@ -9,7 +9,7 @@ process FASTQC {
     tuple val(sample_id), path(reads)
 
     output:
-    path "fastqc_${sample_id}_logs" 
+    path "fastqc_${sample_id}_logs", emit: logs
 
     script:
     """
diff --git a/modules/multiqc/main.nf b/modules/multiqc/main.nf
index a390282..a476ded 100644
--- a/modules/multiqc/main.nf
+++ b/modules/multiqc/main.nf
@@ -9,7 +9,7 @@ process MULTIQC {
     path(config) 
 
     output:
-    path('multiqc_report.html')
+    path('multiqc_report.html'), emit: report
 
     script:
     """