format

src/plassembler/__init__.py

@@ -833,7 +833,7 @@ def run(
 @click.option(
     "--no_copy_numbers",
     help="Only run the PLSDB mash screen, not copy number estimation",
-    is_flag=True
+    is_flag=True,
 )
 def assembled(
     ctx,
@@ -899,7 +899,6 @@ def assembled(
     validate_fastas_assembled_mode(input_chromosome, input_plasmids, no_copy_numbers)
 
     if no_copy_numbers is False:
-
         # check fastqs
         logger.info("Checking input fastqs.")
 
@@ -916,7 +915,13 @@ def assembled(
             if skip_qc is False:
                 logger.info("Filtering long reads with chopper")
                 chopper(  # due to the stdin side of this, just implement the class maually in py
-                    longreads, outdir, min_length, min_quality, long_zipped, threads, logdir
+                    longreads,
+                    outdir,
+                    min_length,
+                    min_quality,
+                    long_zipped,
+                    threads,
+                    logdir,
                 )
 
             else:  # copy the input to the outdir

src/plassembler/utils/plass_class.py

@@ -1097,7 +1097,7 @@ def process_mash_tsv(self, plassembler_db_dir, plasmid_fasta):
 
     def combine_depth_mash_tsvs(self, prefix, no_copy_numbers):
         """
-        Combine depth and mash dataframes - if not --no_copy_numbers 
+        Combine depth and mash dataframes - if not --no_copy_numbers
         :param outdir: output directory
         :return: mash_empty: boolean whether there was a mash hit
         """
@@ -1116,7 +1116,6 @@ def combine_depth_mash_tsvs(self, prefix, no_copy_numbers):
         else:
             combined_depth_mash_df = self.mash_df
 
-
         combined_depth_mash_df.to_csv(
             os.path.join(outdir, prefix + "_summary.tsv"), sep="\t", index=False
         )