fix linting after mergin branch

README.md

@@ -52,8 +52,8 @@ In specific cases where samples recorded in the input samplesheet belong to more
 
 > NOTE: This scenario is supported when [Kmerfinder](https://bitbucket.org/genomicepidemiology/kmerfinder/src/master/) analysis is performed only.
 
-
 In cases where input samplesheet has files where , the pipeline will group samples in batches according to their reference genomes and will provide a general QUAST containing all the input samples and a by reference genome QUAST report, that is, a quast report for each reference genome.
+
 ## Usage
 
 > [!NOTE]

assets/multiqc_config_long.yml

@@ -57,7 +57,6 @@ module_order:
       path_filters:
         - "./bakta/*.txt"
 
-
 report_section_order:
   nanostat:
     after: general_stats
@@ -134,7 +133,6 @@ custom_data:
         format: "{:,.0f}"
 
 export_plots: true
-
 # # Customise the module search patterns to speed up execution time
 # #  - Skip module sub-tools that we are not interested in
 # #  - Replace file-content searching with filename pattern searching

assets/multiqc_config_short.yml

@@ -51,7 +51,6 @@ module_order:
       path_filters:
         - "./bakta/*.txt"
 
-
 report_section_order:
   fastqc:
     after: general_stats

bin/csv_to_yaml.py

@@ -4,27 +4,22 @@
 import csv
 import yaml
 
+
 def parse_args(args=None):
-    Description = (
-        "Create a yaml file from csv input file grouping samples as keys and resting fields as their value pair."
-    )
+    Description = "Create a yaml file from csv input file grouping samples as keys and resting fields as their value pair."
 
     Epilog = "Example usage: python csv_to_yaml.py -i myfile.csv -k 'sample_name' -o converted_file"
     parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
     parser.add_argument(
-        "-i",
-        "--input",
-        type=str,
-        dest="CSV_FILE",
-        help="Input file in CSV format."
+        "-i", "--input", type=str, dest="CSV_FILE", help="Input file in CSV format."
     )
 
     parser.add_argument(
         "-k",
         "--key_field",
         type=str,
         dest="KEY_FIELD",
-        help="Name of the key/column grupping field in the input csv."
+        help="Name of the key/column grupping field in the input csv.",
     )
 
     parser.add_argument(
@@ -33,26 +28,32 @@ def parse_args(args=None):
         type=str,
         default="output_file",
         dest="OUT_PREFIX",
-        help="Output file name"
+        help="Output file name",
     )
     return parser.parse_args(args)
 
+
 def parse_csv(csv_file):
-    with open(csv_file, 'r') as c:
+    with open(csv_file, "r") as c:
         csv_reader = csv.DictReader(c)
-        data = [ row for row in csv_reader]
+        data = [row for row in csv_reader]
     return data
 
+
 def create_yaml(data, key, output_prefix):
-    yaml_data = {entry[key]: {k: v for k, v in entry.items() if k != key} for entry in data}
-    with open( output_prefix + '.yaml' , 'w') as yaml_file:
+    yaml_data = {
+        entry[key]: {k: v for k, v in entry.items() if k != key} for entry in data
+    }
+    with open(output_prefix + ".yaml", "w") as yaml_file:
         yaml.dump(yaml_data, yaml_file, default_flow_style=False)
 
+
 def main(args=None):
     args = parse_args(args)
     file_list = parse_csv(args.CSV_FILE)
 
     create_yaml(data=file_list, key=args.KEY_FIELD, output_prefix=args.OUT_PREFIX)
 
+
 if __name__ == "__main__":
     sys.exit(main())

bin/download_reference.py

@@ -49,15 +49,14 @@
 import argparse
 import os
 
-#import wget
+# import wget
 import requests
 
+
 # TODO: Generate report
 def parse_args(args=None):
-    Description = (
-        "download the reference files \
+    Description = "download the reference files \
         (fna, faa, gff)from the reference NCBI file."
-    )
     Epilog = """Usage example: \
         python download_reference.py \
         -file <file with the references created by find_common_reference> \
@@ -66,17 +65,13 @@ def parse_args(args=None):
 
     parser = argparse.ArgumentParser(description=Description, epilog=Epilog)
     parser.add_argument(
-        "-file",
-        help="File containing the ranking of references from kmerfinder."
+        "-file", help="File containing the ranking of references from kmerfinder."
     )
     parser.add_argument(
         "-reference",
-        help="File containing the paths to bacterial references. See example in: https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt"
-    )
-    parser.add_argument(
-        "-out_dir",
-        help="Output directory."
+        help="File containing the paths to bacterial references. See example in: https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt",
     )
+    parser.add_argument("-out_dir", help="Output directory.")
 
     return parser.parse_args(args)
 
@@ -98,10 +93,9 @@ def download_references(file, reference, out_dir):
         ]
         top_reference = infile[0][0]
 
-    with open(str(top_reference) + ".winner", 'w') as topref:
+    with open(str(top_reference) + ".winner", "w") as topref:
         topref.write(top_reference)
 
-
     # create the outdir (do nothing if already there)
     try:
         os.mkdir(out_dir)
@@ -134,7 +128,11 @@ def download_references(file, reference, out_dir):
                 dir_url.append(assembly_url)
 
         if len(dir_url) == 0:
-            print("No assemblies responding to the top reference: ", top_reference, " were found")
+            print(
+                "No assemblies responding to the top reference: ",
+                top_reference,
+                " were found",
+            )
             sys.exit(1)
 
         dir_url = str(dir_url[0])
@@ -145,9 +143,9 @@ def download_references(file, reference, out_dir):
         file_url = dir_url + r_end
         print(file_url)
 
-        #wget.download(file_url, out_file)
+        # wget.download(file_url, out_file)
         response = requests.get(file_url, stream=True)
-        with open(out_file, 'wb') as out:
+        with open(out_file, "wb") as out:
             for chunk in response.iter_content(chunk_size=8192):
                 out.write(chunk)
 

bin/kmerfinder_summary.py

@@ -15,7 +15,6 @@
 
 
 def check_arg(args=None):
-
     """
     Description:
         Function collect arguments from command line using argparse
@@ -32,14 +31,14 @@ def check_arg(args=None):
     parser = argparse.ArgumentParser(
         prog="07-kmerfinder.py",
         formatter_class=argparse.RawDescriptionHelpFormatter,
-        description="07-kmerfinder.py creates a csv file from results.txt file", # FIXME
+        description="07-kmerfinder.py creates a csv file from results.txt file",  # FIXME
     )
 
     parser.add_argument(
         "--path",
         "-p",
         required=True,
-        help="Insert path of results.txt file like /home/user/Service_folder/ANALYSIS/07-kmerfinder", # FIXME
+        help="Insert path of results.txt file like /home/user/Service_folder/ANALYSIS/07-kmerfinder",  # FIXME
     )
 
     parser.add_argument(
@@ -61,7 +60,6 @@ def check_arg(args=None):
 
 
 def kmerfinder_dictionary(file_txt):
-
     """
     Description:
         Function to extract the relevant part of result.txt file
@@ -71,7 +69,7 @@ def kmerfinder_dictionary(file_txt):
         dictionary
     """
 
-    step = "07-kmerfinder_" # FIXME
+    step = "07-kmerfinder_"  # FIXME
 
     num_lines = sum(1 for line in open(file_txt))
     hits = num_lines - 1  # to count the total number of hits
@@ -110,7 +108,6 @@ def kmerfinder_dictionary(file_txt):
 
 
 def dictionary2bn(dictionary, binary_file):
-
     """
 
     Description:
@@ -134,7 +131,6 @@ def dictionary2bn(dictionary, binary_file):
 
 
 def dictionary2csv(dictionary, csv_file):
-
     """
 
     Description:
@@ -185,7 +181,7 @@ def dictionary2csv(dictionary, csv_file):
     kmer_all = {}
 
     for sample in sample_list:
-        file_name = os.path.join(path, sample + "_results.txt" )
+        file_name = os.path.join(path, sample + "_results.txt")
         kmer_all[sample] = kmerfinder_dictionary(file_name)
 
     print("kmerfinder_dictionary done")