Add CLI argument parsing

src/parser.py

@@ -1,3 +1,4 @@
+from argparse import ArgumentParser
 from glob import glob
 from typing import List, Union
 
@@ -22,10 +23,18 @@ def save_to_file(filename, adapters) -> None:
     adapters.to_csv(filename, index=False, header=False, sep="\n")
 
 
+def parse_arguments():
+    parser = ArgumentParser()
+    parser.add_argument("input", help="directory containing the fastqc reports")
+    parser.add_argument("output", help="file where to export the sequences")
+    return parser.parse_args()
+
+
 def main():
-    file_list = find_html_files("data")
+    args = parse_arguments()
+    file_list = find_html_files(args.input)
     adapters = extract_adapters(file_list)
-    save_to_file("placeholder.txt", adapters)
+    save_to_file(args.output, adapters)
 
 
 if __name__ == "__main__":