DAS Tool can be used with genomes_collection part and remove some useless print and commented lines

magneto/rules/QC.smk

@@ -423,8 +423,9 @@ rule fastP_PE:
         json =  os.path.join(fastp_reports_dir, "{PE}_{run}_{run}_fastp.json"),
         html = os.path.join(fastp_reports_dir, "{PE}_{run}_{run}_fastp.html"),
     input:
-        r1 = os.path.join(path_to_data, "{PE}_R1.fastq.gz"),
-        r2 = os.path.join(path_to_data, "{PE}_R2.fastq.gz"),
+        #get_reads_PE(PE_samples)
+        r1 = os.path.join(path_to_data, "{run}_R1.fastq.gz"),
+        r2 = os.path.join(path_to_data, "{run}_R2.fastq.gz"),
     conda:
         os.path.join(env_dir, "pre-processing.yaml")
     log: