From 1b4d9c3fa1504a56777ffc7870ef388db1cc9978 Mon Sep 17 00:00:00 2001
From: renewiegandt <rene.wiegandt@mpi-bn.mpg.de>
Date: Tue, 16 Apr 2019 10:31:54 +0200
Subject: [PATCH] Reworked check on required parameters

---
 pipeline.nf | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/pipeline.nf b/pipeline.nf
index 1c1230b..2084666 100644
--- a/pipeline.nf
+++ b/pipeline.nf
@@ -89,14 +89,15 @@ val_missing = false
 send_help = false
 missing_params = []
 
-//@TODO remove iteration over all parameter
-params.each { key, value ->
+req_params.each { key ->
 	if (req_params.contains(key)){
-		if (key == "gtf_annotation" && value == "" && params.gtf_merged == ""){
-			val_missing = true
-			missing_params.add("$key or gtf_merged")
+		if (key == "gtf_annotation") {
+			if (params[key] == "" && params.gtf_merged == "") {
+				val_missing = true
+				missing_params.add("$key or gtf_merged")
+			}
 		} else {
-			if (value == ""){
+			if (params[key] == ""){
 				val_missing = true
 				missing_params.add(key)
 			}
@@ -108,6 +109,7 @@ if (val_missing){
 	send_help = true
 	println("Error: Following required parameters are missing: $missing_params")
 }
+
 if (send_help || "${params.help}" != "0") {
 log.info """
 Usage: nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] --config [UROPA-config-file]