remove print

Snakefile

@@ -54,15 +54,10 @@ REQUIREMENTS IN DESIGN:
 # list of all files in the directory 'input_dir'
 
 filenames = [f for f in os.listdir(config["input_dir"]) if match(r'.*'+config["input_mate"]+config["input_extension"]+'', f)] 
-print(filenames)
+
 if not filenames :
     raise ValueError("Please provides input fastq files")
 
-samples = [sub(config["input_mate"]+config["input_extension"], '', file) for file in filenames]
-marks = [ x.strip() for x in (config["design"]["marks"]).split(",")]
-conds = [ x.strip() for x in (config["design"]["condition"]).split(",")]
-rep_flag = config["design"]["replicates"]
-print(samples, marks, conds)
 #-------------------------------------------------------
 # paired-end data gestion
 
@@ -81,7 +76,12 @@ else:
     else:
         raise ValueError("Please provides single or paired files only")
 
-
+#get sample names
+filename_R1 = [ file for file in filenames if match(r'.*'+rt1+config["input_extension"]+'', file)]
+samples = [sub(rt1+config["input_extension"], '', file) for file in filename_R1]
+marks = [ x.strip() for x in (config["design"]["marks"]).split(",")]
+conds = [ x.strip() for x in (config["design"]["condition"]).split(",")]
+rep_flag = config["design"]["replicates"]
 
 # -----------------------------------------------
 # get list of INPUT files