Formatting

workflow/rules/preprocessing.smk

@@ -14,15 +14,16 @@ rule update_sample:
     script:
         "../scripts/update-sample-sheet.py"
 
+
 rule barcode_rename:
     input:
-        barcodes = "barcode-rename.csv",
-        source_dir = config["source_dir"],
-    output: 
-        out_dir = directory(config["output_dir"])
+        barcodes="barcode-rename.csv",
+        source_dir=config["source_dir"],
+    output:
+        out_dir=directory(config["output_dir"]),
     log:
         "logs/barcode_rename.txt",
     conda:
         "../envs/python.yaml"
     script:
-        "../scripts/barcode_rename.py"
+        "../scripts/barcode_rename.py"

workflow/scripts/barcode_rename.py

@@ -6,32 +6,32 @@
 import os
 
 
-def get_barcode_dirs(source_directory, barcode_numbers): 
+def get_barcode_dirs(source_directory, barcode_numbers):
     try:
         barcode_dirs = []
         for barcode_number in barcode_numbers:
-            #Construct the source file path
+            # Construct the source file path
             source_file = f"barcode{barcode_number}"
             source_path = os.path.join(source_directory, source_file)
 
             if os.path.exists(source_path):
                 barcode_dirs.append(source_path)
             else:
                 print(f"Directory '{source_path}' does not exist.")
-        
+
         return barcode_dirs
-    
+
     except Exception as e:
         print(f"An error occurred: {str(e)}")
         return []
 
 
 def concatenate_fastq(bc_directory, outfile):
-    input_files = os.path.join(bc_directory, '*.fastq.gz')
+    input_files = os.path.join(bc_directory, "*.fastq.gz")
     print(input_files)
     out_file = f"{os.path.join(outfile, os.path.split(bc_directory)[1])}_all.fastq"
     print(out_file)
-    subprocess.Popen(f'zcat {input_files} > {out_file}', shell=True).wait()
+    subprocess.Popen(f"zcat {input_files} > {out_file}", shell=True).wait()
 
 
 def run_sample_prep(source_directory, barcode_numbers, outfile):
@@ -42,7 +42,7 @@ def run_sample_prep(source_directory, barcode_numbers, outfile):
 
 
 def rename_files(final_dir):
-    # rename files 
+    # rename files
     renames = pd.read_csv(barcode_csv)
     renames.reset_index(drop=True, inplace=True)
 
@@ -54,10 +54,13 @@ def rename_files(final_dir):
     for file in files:
         num = file.split("_")[0][-2:]
         print(num)
-        print(final_dir + file + " " + final_dir + str(rename_dict[int(num)]) + ".fastq")
+        print(
+            final_dir + file + " " + final_dir + str(rename_dict[int(num)]) + ".fastq"
+        )
         os.rename(final_dir + file, final_dir + str(rename_dict[int(num)]) + ".fastq")
     print(files)
 
+
 config = snakemake.config
 
 barcode_csv = str(snakemake.input.barcodes)
@@ -72,7 +75,7 @@ def rename_files(final_dir):
     os.makedirs(out_dir)
 
 # getting barcode numbers
-barcode_csv_ = pd.read_csv(barcode_csv, dtype={'barcode': str})
+barcode_csv_ = pd.read_csv(barcode_csv, dtype={"barcode": str})
 used_barcodes = barcode_csv_["barcode"]
 
 run_sample_prep(source_path, used_barcodes, out_dir)