From ef4f78ea460fb3084086a8cb7ea7c3935f7c8ce4 Mon Sep 17 00:00:00 2001
From: MarieLataretu <marie.lataretu@uni-jena.de>
Date: Thu, 25 Nov 2021 17:33:02 +0100
Subject: [PATCH] problem when input files end with clean Fixes #46

---
 clean.nf | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/clean.nf b/clean.nf
index fecd4f7..093074c 100755
--- a/clean.nf
+++ b/clean.nf
@@ -15,6 +15,9 @@ def parameter_diff = params.keySet() - valid_params
 if (parameter_diff.size() != 0){
     exit 1, "ERROR: Parameter(s) $parameter_diff is/are not valid in the pipeline!\n"
 }
+if (params.illumina_single_end.contains('.clean.') || params.illumina.contains('.clean.') || params.nano.contains('.clean.') || params.fasta.contains('.clean.') ) { 
+  exit 1, "ERROR: Input files cannot contain `.clean.`\n" 
+}
 
 /************************** 
 * META & HELP MESSAGES