From cd8aacc80887ecd087f5950cadfb75c3d84fa854 Mon Sep 17 00:00:00 2001
From: drpatelh <drhpatel@gmail.com>
Date: Thu, 3 Dec 2020 17:46:29 +0000
Subject: [PATCH] Fix InvocationTargetException by not using checkIfExists

---
 modules/local/process/samplesheet_check.nf | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/modules/local/process/samplesheet_check.nf b/modules/local/process/samplesheet_check.nf
index 62a204deb..869739afe 100644
--- a/modules/local/process/samplesheet_check.nf
+++ b/modules/local/process/samplesheet_check.nf
@@ -35,10 +35,16 @@ def get_samplesheet_paths(LinkedHashMap row) {
     meta.strandedness = row.strandedness
 
     def array = []
+    if (!file(row.fastq_1).exists()) {
+        exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}"
+    }
     if (meta.single_end) {
-        array = [ meta, [ file(row.fastq_1, checkIfExists: true) ] ]
+        array = [ meta, [ file(row.fastq_1) ] ]
     } else {
-        array = [ meta, [ file(row.fastq_1, checkIfExists: true), file(row.fastq_2, checkIfExists: true) ] ]
+        if (!file(row.fastq_2).exists()) {
+            exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
+        }
+        array = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
     }
     return array
 }