Fix bug with reading scaffolds files from sample sheet

bin/import_jovian_output.py

@@ -136,6 +136,7 @@ Output: a list of files to move or copy.
             missing_scaffolds_files = 0
             
             trimmed_reads_files = []
+            filtered_scaffolds_files = []
 
             for sample in SAMPLES:
                 forward_filename = sample + "_pR1.fq"
@@ -165,8 +166,6 @@ Output: a list of files to move or copy.
                     print("Unpaired trimmed reads for sample %s were not found." % sample)
                     missing_trimmed_files += 1
 
-                filtered_scaffolds_files = []
-
                 #NOTE: I assume the default 500 nt cutoff for scaffold length
                 scaffold_filename = sample + "_scaffolds_ge500nt.fasta"
                 filtered_scaffolds_file = input_dir / "data" / "scaffolds_filtered" / scaffold_filename