Create a script that executes the pipeline

generation.sh

@@ -16,6 +16,6 @@ prefix="curesim_"
 Rscript src/repertoire.r "$sequences"
 
 for file in "$data_directory"*.fastq; do
-	file_name=$(cut -d / -f 2)
+	file_name=$(echo "$file" | cut -d / -f 2)
 	java -jar tools/CuReSim.jar -f "$file" -o "$data_directory$prefix$file_name"
 done