From 78e4e5550d35509ee3f8f50168f5731bcab2993c Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Wed, 12 May 2021 15:15:33 +0200
Subject: [PATCH] fix log4bash warning + added missing track and trace command

---
 bin/copyRawDataToPrm.sh | 20 ++++++++++++--------
 bin/notifications.sh    |  4 ++--
 2 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/bin/copyRawDataToPrm.sh b/bin/copyRawDataToPrm.sh
index adc467fa..7be6d74f 100755
--- a/bin/copyRawDataToPrm.sh
+++ b/bin/copyRawDataToPrm.sh
@@ -300,12 +300,11 @@ function splitSamplesheetPerProject() {
 	#  * either only demultiplexing was requested via the samplesheet
 	#  * or when disabled on the commandline by enabling "archiveMode".
 	#
-	if [[ "${archiveMode}" == 'false' ]]; then
-		for _project in "${_projects[@]}"
-		do
-			
-			printf '%s\n' "${_project},${_run},,,,,," \
-				>> "${JOB_CONTROLE_FILE_BASE}.trace_post_projects.csv"
+	
+	for _project in "${_projects[@]}"
+	do
+		
+		if [[ "${archiveMode}" == 'false' ]]; then
 			#
 			# Skip project if demultiplexing only.
 			#
@@ -321,11 +320,16 @@ function splitSamplesheetPerProject() {
 				mv "${_projectSampleSheet}"{.tmp,}
 				log4Bash 'INFO' "${LINENO}" "${FUNCNAME:-main}" '0' "Created ${_projectSampleSheet}."
 			fi
-		done
-	fi
+		fi
+		printf '%s\n' "${_project},${_run},,,,,," \
+			>> "${JOB_CONTROLE_FILE_BASE}.trace_post_projects.csv"
+		
+	done
+
 	#
 	# Track and Trace.
 	#
+	
 	local _allProjects
 	_allProjects="${_projects[*]}"
 	_allProjects="${_allProjects// /,}"
diff --git a/bin/notifications.sh b/bin/notifications.sh
index 9d051e58..bc06b164 100755
--- a/bin/notifications.sh
+++ b/bin/notifications.sh
@@ -206,8 +206,8 @@ function notification() {
 		#
 		if [[ ! -e "${_controlFileBase}.trackAndTrace.failed" && ! -e "${_controlFileBase}.sendEmail.failed" ]]
 		then 
-			log4Bash 'INFO' "${LINENO}" "${FUNCNAME[0]:-main}" '0' "${SCRIPT_NAME} succeeded for the last processed phase:state combination (for which notifications were configured) of ${_project}/${_run}." \
-			log4Bash 'INFO' "${LINENO}" "${FUNCNAME[0]:-main}" '0' "               Beware that notifications for previously processed phase:state combinations may have failed."
+			log4Bash 'INFO' "${LINENO}" "${FUNCNAME[0]:-main}" '0' "${SCRIPT_NAME} succeeded for the last processed phase:state combination (for which notifications were configured) of ${_project}/${_run}."
+			log4Bash 'INFO' "${LINENO}" "${FUNCNAME[0]:-main}" '0' "Beware that notifications for previously processed phase:state combinations may have failed."
 
 			log4Bash 'DEBUG' "${LINENO}" "${FUNCNAME[0]:-main}" '0' "Created ${JOB_CONTROLE_FILE_BASE}.finished."
 		else