From da8d7c0ac632e57222e704c4a32ada1e14fefb57 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Fri, 10 Jan 2025 15:17:56 +0100
Subject: [PATCH 01/31] Fixed path to files not containing sample name in
 basename

---
 relecov_tools/conf/bioinfo_config.json |  4 ++++
 relecov_tools/read_bioinfo_metadata.py | 12 ++++++++----
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/relecov_tools/conf/bioinfo_config.json b/relecov_tools/conf/bioinfo_config.json
index 8e5747b6..3867336c 100644
--- a/relecov_tools/conf/bioinfo_config.json
+++ b/relecov_tools/conf/bioinfo_config.json
@@ -6,6 +6,7 @@
             "header_row_idx": 1,
             "required": true,
             "function": null,
+            "multiple_samples": true,
             "split_by_batch": true,
             "content": {
                 "analysis_date": "analysis_date",
@@ -44,6 +45,7 @@
             "sample_col_idx": 1,
             "header_row_idx": 1,
             "required": true,
+            "multiple_samples": true,
             "split_by_batch": true,
             "function": "parse_long_table",
             "content": {
@@ -84,6 +86,7 @@
             "fn": "summary_variants_metrics_mqc.csv",
             "sample_col_idx": 1,
             "header_row_idx": 1,
+            "multiple_samples": true,
             "required": true,
             "function": null,
             "content": {
@@ -100,6 +103,7 @@
         "workflow_summary": {
             "fn": "multiqc_report.html",
             "required": true,
+            "multiple_samples": true,
             "function": null,
             "content": {
                 "software_version": {
diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index 98aa0b9f..138b61d0 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -601,6 +601,7 @@ def add_bioinfo_files_path(self, files_found_dict, j_data):
         """
         method_name = f"{self.add_bioinfo_files_path.__name__}"
         sample_name_error = 0
+        multiple_sample_files = self.get_multiple_sample_files()
         for row in j_data:
             row["bioinfo_metadata_file"] = self.out_filename
             if not row.get("sequencing_sample_id"):
@@ -614,10 +615,13 @@ def add_bioinfo_files_path(self, files_found_dict, j_data):
             for key, values in files_found_dict.items():
                 file_path = "Not Provided [GENEPIO:0001668]"
                 if values:  # Check if value is not empty
-                    for file in values:
-                        if sample_name in file:
-                            file_path = file
-                            break  # Exit loop if match found
+                    if key in multiple_sample_files:
+                        file_path = values[0]
+                    else:
+                        for file in values:
+                            if sample_name in file:
+                                file_path = file
+                                break  # Exit loop if match found
                 path_key = f"{self.software_name}_filepath_{key}"
                 row[path_key] = file_path
                 if self.software_config[key].get("extract"):

From 8eede463a0b22b8966d6ab040dbb9437f9a8b6f6 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Mon, 13 Jan 2025 13:08:34 +0100
Subject: [PATCH 02/31] Added batchID/date to filenames instead of date

---
 relecov_tools/assets/pipeline_utils/viralrecon.py | 13 ++++++-------
 relecov_tools/read_bioinfo_metadata.py            | 11 ++++++-----
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/relecov_tools/assets/pipeline_utils/viralrecon.py b/relecov_tools/assets/pipeline_utils/viralrecon.py
index eb0ff96d..4371b133 100644
--- a/relecov_tools/assets/pipeline_utils/viralrecon.py
+++ b/relecov_tools/assets/pipeline_utils/viralrecon.py
@@ -153,10 +153,9 @@ def convert_to_json(self, samp_dict):
             j_list.append(j_dict)
         return j_list
 
-    def save_to_file(self, j_list):
+    def save_to_file(self, j_list, batch_date):
         """Transform the parsed data into a json file"""
-        date_now = datetime.now().strftime("%Y%m%d%H%M%S")
-        file_name = "long_table_" + date_now + ".json"
+        file_name = "long_table_" + batch_date + ".json"
         file_path = os.path.join(self.output_directory, file_name)
 
         try:
@@ -180,7 +179,7 @@ def parsing_csv(self):
 
 
 # START util functions
-def handle_pangolin_data(files_list, output_folder=None):
+def handle_pangolin_data(files_list, batch_date, output_folder=None):
     """File handler to parse pangolin data (csv) into JSON structured format.
 
     Args:
@@ -320,7 +319,7 @@ def get_pango_data_version(files_list):
     return pango_data_processed
 
 
-def parse_long_table(files_list, output_folder=None):
+def parse_long_table(files_list, batch_id, output_folder=None):
     """File handler to retrieve data from long table files and convert it into a JSON structured format.
     This function utilizes the LongTableParse class to parse the long table data.
     Since this utility handles and maps data using a custom way, it returns None to be avoid being  transferred to method read_bioinfo_metadata.BioinfoMetadata.mapping_over_table().
@@ -349,7 +348,7 @@ def parse_long_table(files_list, output_folder=None):
         # Parsing long table data and saving it
         long_table_data = long_table.parsing_csv()
         # Saving long table data into a file
-        long_table.save_to_file(long_table_data)
+        long_table.save_to_file(long_table_data, batch_id)
         stderr.print("[green]\tProcess completed")
     elif len(files_list) > 1:
         method_log_report.update_log_report(
@@ -361,7 +360,7 @@ def parse_long_table(files_list, output_folder=None):
     return None
 
 
-def handle_consensus_fasta(files_list, output_folder=None):
+def handle_consensus_fasta(files_list, batch_id, output_folder=None):
     """File handler to parse consensus data (fasta) into JSON structured format.
 
     Args:
diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index 138b61d0..21a0bc34 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -232,7 +232,7 @@ def validate_software_mandatory_files(self, files_dict):
         self.log_report.print_log_report(method_name, ["valid", "warning"])
         return
 
-    def add_bioinfo_results_metadata(self, files_dict, j_data, output_folder=None):
+    def add_bioinfo_results_metadata(self, files_dict, j_data, batch_id, output_folder=None):
         """Adds metadata from bioinformatics results to j_data.
         It first calls file_handlers and then maps the handled
         data into j_data.
@@ -241,6 +241,7 @@ def add_bioinfo_results_metadata(self, files_dict, j_data, output_folder=None):
             files_dict (dict{str:str}): A dictionary containing file paths found based on the definitions provided in the bioinformatic JSON file within the software scope (self.software_config).
             j_data (list(dict{str:str}): A list of dictionaries containing metadata lab (list item per sample).
             output_folder (str): Path to save output files generated during handling_files() process.
+            batch_id(str): ID of the batch which corresponds with the data download date.
 
         Returns:
             j_data_mapped: A list of dictionaries with bioinformatics metadata mapped into j_data.
@@ -263,7 +264,7 @@ def add_bioinfo_results_metadata(self, files_dict, j_data, output_folder=None):
                 )
                 continue
             # Handling files
-            data_to_map = self.handling_files(files_dict[key], output_folder)
+            data_to_map = self.handling_files(files_dict[key], output_folder, batch_id)
             # Mapping data to j_data
             mapping_fields = self.software_config[key].get("content")
             if not mapping_fields:
@@ -324,7 +325,7 @@ def handling_tables(self, file_list, conf_tab_name):
             sys.exit(self.log_report.print_log_report(method_name, ["error"]))
         return data
 
-    def handling_files(self, file_list, output_folder):
+    def handling_files(self, file_list, output_folder, batch_id):
         """Handles different file formats to extract data regardless of their structure.
         The goal is to extract the data contained in files specified in ${file_list},
         using either 'standard' handlers defined in this class or pipeline-specific file handlers.
@@ -368,7 +369,7 @@ def handling_files(self, file_list, output_folder):
                 import_statement = f"import {utils_name}"
                 exec(import_statement)
                 # Get method name and execute it.
-                data = eval(utils_name + "." + func_name + "(file_list, output_folder)")
+                data = eval(utils_name + "." + func_name + "(file_list, batch_id, output_folder)")
             except Exception as e:
                 self.log_report.update_log_report(
                     self.add_bioinfo_results_metadata.__name__,
@@ -801,7 +802,7 @@ def create_bioinfo_file(self):
             batch_data = batch_dict["j_data"]
             stderr.print("[blue]Adding bioinfo metadata to read lab metadata...")
             batch_data = self.add_bioinfo_results_metadata(
-                files_found_dict, batch_data, batch_dir
+                files_found_dict, batch_data, batch_date, batch_dir
             )
             stderr.print("[blue]Adding software versions to read lab metadata...")
             batch_data = self.get_multiqc_software_versions(

From ea5a94740f3f1f3c95ea3ffbe7f040d9603138a4 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Mon, 13 Jan 2025 13:10:17 +0100
Subject: [PATCH 03/31] add current date to splitted files

---
 relecov_tools/read_bioinfo_metadata.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index 21a0bc34..2f142557 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -6,6 +6,7 @@
 import re
 import shutil
 from bs4 import BeautifulSoup
+from datetime import datetime
 
 import pandas as pd
 import relecov_tools.utils
@@ -740,7 +741,7 @@ def split_tables_by_batch(self, files_found_dict, batch_data, output_dir):
             output_dir (str): Output location for the generated tabular file
         """
 
-        def extract_batch_rows_to_file(file):
+        def extract_batch_rows_to_file(file, sufix):
             """Create a new table file only with rows matching samples in batch_data"""
             extdict = {".csv": ",", ".tsv": "\t", ".tab": "\t"}
             file_extension = os.path.splitext(file)[1]
@@ -750,14 +751,18 @@ def extract_batch_rows_to_file(file):
             sample_col = file_df.columns[sample_colpos]
             file_df[sample_col] = file_df[sample_col].astype(str)
             file_df = file_df[file_df[sample_col].isin(batch_samples)]
+            
+            base, ext = os.path.splitext(os.path.basename(file))
+            new_filename = f"{base}_{sufix}{ext}"
             output_path = os.path.join(
-                output_dir, "analysis_results", os.path.basename(file)
+                output_dir, "analysis_results", new_filename
             )
             file_df.to_csv(output_path, index=False, sep=extdict.get(file_extension))
             return
 
         method_name = self.split_tables_by_batch.__name__
         namekey = "sequencing_sample_id"
+        sufix = datetime.now().strftime("%Y%m%d%H%M%S")
         batch_samples = [row.get(namekey) for row in batch_data]
         for key, files in files_found_dict.items():
             if not self.software_config[key].get("split_by_batch"):
@@ -766,7 +771,7 @@ def extract_batch_rows_to_file(file):
             sample_colpos = self.get_sample_idx_colpos(key)
             for file in files:
                 try:
-                    extract_batch_rows_to_file(file)
+                    extract_batch_rows_to_file(file,sufix)
                 except Exception as e:
                     if self.software_config[key].get("required"):
                         log_type = "error"

From d7a1516ee522d51ab58d98659e2c382d9af0dd9d Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Mon, 13 Jan 2025 13:10:52 +0100
Subject: [PATCH 04/31] add year to outdir path

---
 relecov_tools/read_bioinfo_metadata.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index 2f142557..9c6c5434 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -831,6 +831,11 @@ def create_bioinfo_file(self):
                 )
             log.info("Created output json file: %s" % batch_filepath)
             stderr.print(f"[green]Created batch json file: {batch_filepath}")
+
+        year = str(datetime.now().year)
+        out_path = os.path.join(self.output_folder, year)
+        os.makedirs(out_path, exist_ok=True)
+
         stderr.print("[blue]Writting output json file")
         os.makedirs(self.output_folder, exist_ok=True)
         file_path = os.path.join(self.output_folder, self.out_filename)

From 48a6185441474b2a3b236942b3444c52e21dc89e Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Mon, 13 Jan 2025 13:11:53 +0100
Subject: [PATCH 05/31] test whether samples correspond to same batch date or
 not

---
 relecov_tools/read_bioinfo_metadata.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index 9c6c5434..edf39946 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -800,6 +800,19 @@ def create_bioinfo_file(self):
         self.validate_software_mandatory_files(files_found_dict)
         # Split files found based on each batch of samples
         data_by_batch = self.split_data_by_batch(self.j_data)
+        batch_dates = []
+        #Get batch date for all the samples
+        for batch_dir, batch_dict in data_by_batch.items():
+            if batch_dir.split("/")[-1] not in batch_dates:
+                batch_dates.append(batch_dir.split("/")[-1])
+
+        if len(batch_dates) == 1:
+            batch_dates = str(batch_dates[0])
+        else:
+            stderr.print(f"[orange]More than one batch date in the same json data. Using current date as batch date.")
+            log.info("]More than one batch date in the same json data. Using current date as batch date.")
+            batch_dates = datetime.now().strftime("%Y%m%d%H%M%S")
+
         # Add bioinfo metadata to j_data
         for batch_dir, batch_dict in data_by_batch.items():
             self.log_report.logsum.feed_key(batch_dir)

From ffbf5986ad8ab19fe60d5c36da7e976c2ddb8279 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Mon, 13 Jan 2025 13:14:34 +0100
Subject: [PATCH 06/31] Added function to save splitted files to outdir

---
 relecov_tools/read_bioinfo_metadata.py | 47 ++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index edf39946..8830f6a4 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -785,6 +785,49 @@ def extract_batch_rows_to_file(file, sufix):
         self.log_report.print_log_report(method_name, ["valid", "warning", "error"])
         return
 
+    def save_splitted_files(self, files_dict, batch_date, output_folder=None):
+        """
+        Process and save files that where split by batch and that have a function to be processed
+
+        Args:
+            files_dict (dict): A dictionary containing file paths identified for each configuration item.
+            batch_date (str): Date or ID of the batch to be used in the output file name.
+            output_folder (str): Path to save output files generated during processing.
+
+        Returns:
+            None
+        """
+        method_name = f"{self.save_splitted_files.__name__}"
+        for key, config in self.software_config.items():
+            func_name = config.get("function")
+            # Skip configurations that do not match the conditions
+            if config.get("split_by_batch") is True and func_name:
+                try:
+                    file_path = files_dict[key]
+                    stderr.print(f"[blue]Processing splitted file: {file_path}")
+                except KeyError:
+                    self.log_report.update_log_report(
+                        method_name,
+                        "warning",
+                        f"No file path found for '{file_path}'",
+                    )
+                    continue
+                try:
+                    # Dynamically import the function from the specified module
+                    utils_name = f"relecov_tools.assets.pipeline_utils.{self.software_name}"
+                    import_statement = f"import {utils_name}"
+                    exec(import_statement)
+                    # Get method name and execute it.
+                    data = eval(utils_name + "." + func_name + "(file_path, batch_date, output_folder)")
+                except Exception as e:
+                    self.log_report.update_log_report(
+                        self.save_splitted_files.__name__,
+                        "error",
+                        f"Error occurred while parsing '{func_name}': {e}.",
+                    )
+                    sys.exit(self.log_report.print_log_report(method_name, ["error"]))
+        return
+    
     def create_bioinfo_file(self):
         """Create the bioinfodata json with collecting information from lab
         metadata json, mapping_stats, and more information from the files
@@ -849,6 +892,10 @@ def create_bioinfo_file(self):
         out_path = os.path.join(self.output_folder, year)
         os.makedirs(out_path, exist_ok=True)
 
+        stderr.print("[blue]Saving previously splitted files to output directory")
+
+        self.save_splitted_files(files_found_dict, batch_dates, out_path)
+        batch_filename = tag + batch_dates + ".json"
         stderr.print("[blue]Writting output json file")
         os.makedirs(self.output_folder, exist_ok=True)
         file_path = os.path.join(self.output_folder, self.out_filename)

From 2b0447eb93a70f1113d9f4a7152ab0226f421041 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Mon, 13 Jan 2025 13:15:26 +0100
Subject: [PATCH 07/31] test if bioinfo_lab_metadata exist, if exists merge

---
 relecov_tools/read_bioinfo_metadata.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index 8830f6a4..b2629243 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -892,14 +892,19 @@ def create_bioinfo_file(self):
         out_path = os.path.join(self.output_folder, year)
         os.makedirs(out_path, exist_ok=True)
 
+        tag = "bioinfo_lab_metadata_"
         stderr.print("[blue]Saving previously splitted files to output directory")
 
         self.save_splitted_files(files_found_dict, batch_dates, out_path)
         batch_filename = tag + batch_dates + ".json"
         stderr.print("[blue]Writting output json file")
-        os.makedirs(self.output_folder, exist_ok=True)
-        file_path = os.path.join(self.output_folder, self.out_filename)
-        relecov_tools.utils.write_json_fo_file(self.j_data, file_path)
+        file_path = os.path.join(out_path, batch_filename)
+        if os.path.exists(file_path):
+            stderr.print(f"[blue]Bioinfo metadata {file_path} file already exists. Merging new data if possible.")
+            log.info("Bioinfo metadata %s file already exists. Merging new data if possible." % file_path)
+            batch_data = self.merge_metadata(file_path, self.j_data)
+        else:
+            relecov_tools.utils.write_json_fo_file(self.j_data, file_path)
         stderr.print(f"[green]Sucessful creation of bioinfo analyis file: {file_path}")
         self.log_report.logsum.create_error_summary(
             called_module="read-bioinfo-metadata", logs=self.log_report.logsum.logs

From 1d30be21054ae3ab23f1ecc0f40df2ac29bee4b0 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Mon, 13 Jan 2025 13:18:44 +0100
Subject: [PATCH 08/31] Created code to merge metadata if already exist

---
 relecov_tools/read_bioinfo_metadata.py | 39 ++++++++++++++++++++++++--
 1 file changed, 36 insertions(+), 3 deletions(-)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index b2629243..5f5f60f6 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -785,6 +785,34 @@ def extract_batch_rows_to_file(file, sufix):
         self.log_report.print_log_report(method_name, ["valid", "warning", "error"])
         return
 
+    def merge_metadata(self, batch_filepath, batch_data):
+        """
+        Merge metadata json if sample does not exist in the metadata file
+
+        Args:
+            batch_filepath (str): Path to save the json file with the metadata.
+            batch_data (dict): A dictionary containing metadata of the samples.
+        Returns:
+            None
+        """        
+        merged_metadata = relecov_tools.utils.read_json_file(batch_filepath)
+        prev_metadata_dict = {item["sequencing_sample_id"]: item for item in merged_metadata}
+        for item in batch_data:
+            sample_id = item["sequencing_sample_id"]
+            if sample_id in prev_metadata_dict:
+                # When sample already in metadata, checking whether dictionary is the same
+                if prev_metadata_dict[sample_id] != item:
+                    stderr.print(f"[red] Sample {sample_id} has different data in {batch_filepath} and new metadata. Can't merge.")
+                    log.error(
+                        "Sample %s has different data in %s and new metadata. Can't merge." % (sample_id, batch_filepath)
+                    )
+                    sys.exit(1)
+            else:
+                merged_metadata.append(item)
+
+        relecov_tools.utils.write_json_fo_file(merged_metadata, batch_filepath)
+        return merged_metadata
+
     def save_splitted_files(self, files_dict, batch_date, output_folder=None):
         """
         Process and save files that where split by batch and that have a function to be processed
@@ -858,6 +886,8 @@ def create_bioinfo_file(self):
 
         # Add bioinfo metadata to j_data
         for batch_dir, batch_dict in data_by_batch.items():
+            lab_code = batch_dir.split("/")[-2]
+            batch_date = batch_dir.split("/")[-1]
             self.log_report.logsum.feed_key(batch_dir)
             stderr.print(f"[blue]Processing data from {batch_dir}")
             batch_data = batch_dict["j_data"]
@@ -875,12 +905,15 @@ def create_bioinfo_file(self):
             stderr.print("[blue]Adding files path to read lab metadata")
             batch_data = self.add_bioinfo_files_path(files_found_dict, batch_data)
             self.split_tables_by_batch(files_found_dict, batch_data, batch_dir)
-            lab_code = batch_dir.split("/")[-2]
-            batch_date = batch_dir.split("/")[-1]
             tag = "bioinfo_lab_metadata_"
             batch_filename = tag + lab_code + "_" + batch_date + ".json"
             batch_filepath = os.path.join(batch_dir, batch_filename)
-            relecov_tools.utils.write_json_fo_file(batch_data, batch_filepath)
+            if os.path.exists(batch_filepath):
+                stderr.print(f"[blue]Bioinfo metadata {batch_filepath} file already exists. Merging new data if possible.")
+                log.info("Bioinfo metadata %s file already exists. Merging new data if possible." % batch_filepath)
+                batch_data = self.merge_metadata(batch_filepath, batch_data)
+            else:
+                relecov_tools.utils.write_json_fo_file(batch_data, batch_filepath)
             for sample in batch_data:
                 self.log_report.logsum.feed_key(
                     key=batch_dir, sample=sample.get("sequencing_sample_id")

From e9b04da95df4e05891512db238f923ee872b6ae3 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Mon, 13 Jan 2025 13:19:54 +0100
Subject: [PATCH 09/31] created function to search files containing muiltiple
 samples

---
 relecov_tools/read_bioinfo_metadata.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index 5f5f60f6..8b2287be 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -856,6 +856,14 @@ def save_splitted_files(self, files_dict, batch_date, output_folder=None):
                     sys.exit(self.log_report.print_log_report(method_name, ["error"]))
         return
     
+    def get_multiple_sample_files(self):
+        method_name = f"{self.add_bioinfo_files_path.__name__}:{self.get_multiple_sample_files.__name__}"
+        multiple_sample_files = []
+        for key in self.software_config.keys():
+            if self.software_config[key].get("multiple_samples"):
+                multiple_sample_files.append(key)
+        return multiple_sample_files
+
     def create_bioinfo_file(self):
         """Create the bioinfodata json with collecting information from lab
         metadata json, mapping_stats, and more information from the files

From f61e5389bfa074cfa6093383d9e5a68797793601 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Mon, 13 Jan 2025 13:20:13 +0100
Subject: [PATCH 10/31] test whether file exist and try to merge

---
 .../assets/pipeline_utils/viralrecon.py       | 35 +++++++++++++++----
 1 file changed, 29 insertions(+), 6 deletions(-)

diff --git a/relecov_tools/assets/pipeline_utils/viralrecon.py b/relecov_tools/assets/pipeline_utils/viralrecon.py
index 4371b133..6c0eedd0 100644
--- a/relecov_tools/assets/pipeline_utils/viralrecon.py
+++ b/relecov_tools/assets/pipeline_utils/viralrecon.py
@@ -157,13 +157,36 @@ def save_to_file(self, j_list, batch_date):
         """Transform the parsed data into a json file"""
         file_name = "long_table_" + batch_date + ".json"
         file_path = os.path.join(self.output_directory, file_name)
+        if os.path.exists(file_path):
+            stderr.print(f"[blue]Long table {file_path} file already exists. Merging new data if possible.")
+            log.info("Long table %s file already exists. Merging new data if possible." % file_path)
+            original_table = relecov_tools.utils.read_json_file(file_path)
+            samples_indict = {item["sample_name"]: item for item in original_table}
+            for item in j_list:
+                sample_name = item["sample_name"]
+                if sample_name in samples_indict:
+                    if samples_indict[sample_name] != item:
+                        stderr.print(f"[red]Same sample has different data in both long tables.")
+                        log.error(
+                            "Sample %s has different data in %s and new long table. Can't merge." % (sample_name, file_path)
+                            )
+                        return None
+                else:
+                    original_table.append(item)
+            try:
+                with open(file_path, "w") as fh:
+                    fh.write(json.dumps(original_table, indent=4))
+                stderr.print("[green]\tParsed data successfully saved to file:", file_path)
+            except Exception as e:
+                stderr.print("[red]\tError saving parsed data to file:", str(e))
 
-        try:
-            with open(file_path, "w") as fh:
-                fh.write(json.dumps(j_list, indent=4))
-            stderr.print("[green]\tParsed data successfully saved to file:", file_path)
-        except Exception as e:
-            stderr.print("[red]\tError saving parsed data to file:", str(e))
+        else:
+            try:
+                with open(file_path, "w") as fh:
+                    fh.write(json.dumps(j_list, indent=4))
+                stderr.print("[green]\tParsed data successfully saved to file:", file_path)
+            except Exception as e:
+                stderr.print("[red]\tError saving parsed data to file:", str(e))
 
     def parsing_csv(self):
         """

From f226a8cf33a241e39b2948bfe16494e3bf23504f Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Mon, 13 Jan 2025 13:21:52 +0100
Subject: [PATCH 11/31] fixed black

---
 .../assets/pipeline_utils/viralrecon.py       | 32 +++++---
 relecov_tools/read_bioinfo_metadata.py        | 73 +++++++++++++------
 2 files changed, 74 insertions(+), 31 deletions(-)

diff --git a/relecov_tools/assets/pipeline_utils/viralrecon.py b/relecov_tools/assets/pipeline_utils/viralrecon.py
index 6c0eedd0..c71009c6 100644
--- a/relecov_tools/assets/pipeline_utils/viralrecon.py
+++ b/relecov_tools/assets/pipeline_utils/viralrecon.py
@@ -158,25 +158,35 @@ def save_to_file(self, j_list, batch_date):
         file_name = "long_table_" + batch_date + ".json"
         file_path = os.path.join(self.output_directory, file_name)
         if os.path.exists(file_path):
-            stderr.print(f"[blue]Long table {file_path} file already exists. Merging new data if possible.")
-            log.info("Long table %s file already exists. Merging new data if possible." % file_path)
+            stderr.print(
+                f"[blue]Long table {file_path} file already exists. Merging new data if possible."
+            )
+            log.info(
+                "Long table %s file already exists. Merging new data if possible."
+                % file_path
+            )
             original_table = relecov_tools.utils.read_json_file(file_path)
             samples_indict = {item["sample_name"]: item for item in original_table}
             for item in j_list:
                 sample_name = item["sample_name"]
                 if sample_name in samples_indict:
                     if samples_indict[sample_name] != item:
-                        stderr.print(f"[red]Same sample has different data in both long tables.")
+                        stderr.print(
+                            f"[red]Same sample has different data in both long tables."
+                        )
                         log.error(
-                            "Sample %s has different data in %s and new long table. Can't merge." % (sample_name, file_path)
-                            )
+                            "Sample %s has different data in %s and new long table. Can't merge."
+                            % (sample_name, file_path)
+                        )
                         return None
                 else:
                     original_table.append(item)
             try:
                 with open(file_path, "w") as fh:
                     fh.write(json.dumps(original_table, indent=4))
-                stderr.print("[green]\tParsed data successfully saved to file:", file_path)
+                stderr.print(
+                    "[green]\tParsed data successfully saved to file:", file_path
+                )
             except Exception as e:
                 stderr.print("[red]\tError saving parsed data to file:", str(e))
 
@@ -184,7 +194,9 @@ def save_to_file(self, j_list, batch_date):
             try:
                 with open(file_path, "w") as fh:
                     fh.write(json.dumps(j_list, indent=4))
-                stderr.print("[green]\tParsed data successfully saved to file:", file_path)
+                stderr.print(
+                    "[green]\tParsed data successfully saved to file:", file_path
+                )
             except Exception as e:
                 stderr.print("[red]\tError saving parsed data to file:", str(e))
 
@@ -311,9 +323,9 @@ def get_pango_data_version(files_list):
                 )
                 # Add custom content in pangolin
                 pango_data_key = next(iter(pango_data))
-                pango_data[pango_data_key]["lineage_analysis_date"] = (
-                    relecov_tools.utils.get_file_date(pango_file)
-                )
+                pango_data[pango_data_key][
+                    "lineage_analysis_date"
+                ] = relecov_tools.utils.get_file_date(pango_file)
                 pango_data[pango_data_key]["pangolin_database_version"] = pango_data_v
                 # Rename key in f_data
                 pango_data_updated = {
diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index 8b2287be..4d3a284e 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -233,7 +233,9 @@ def validate_software_mandatory_files(self, files_dict):
         self.log_report.print_log_report(method_name, ["valid", "warning"])
         return
 
-    def add_bioinfo_results_metadata(self, files_dict, j_data, batch_id, output_folder=None):
+    def add_bioinfo_results_metadata(
+        self, files_dict, j_data, batch_id, output_folder=None
+    ):
         """Adds metadata from bioinformatics results to j_data.
         It first calls file_handlers and then maps the handled
         data into j_data.
@@ -370,7 +372,12 @@ def handling_files(self, file_list, output_folder, batch_id):
                 import_statement = f"import {utils_name}"
                 exec(import_statement)
                 # Get method name and execute it.
-                data = eval(utils_name + "." + func_name + "(file_list, batch_id, output_folder)")
+                data = eval(
+                    utils_name
+                    + "."
+                    + func_name
+                    + "(file_list, batch_id, output_folder)"
+                )
             except Exception as e:
                 self.log_report.update_log_report(
                     self.add_bioinfo_results_metadata.__name__,
@@ -751,12 +758,10 @@ def extract_batch_rows_to_file(file, sufix):
             sample_col = file_df.columns[sample_colpos]
             file_df[sample_col] = file_df[sample_col].astype(str)
             file_df = file_df[file_df[sample_col].isin(batch_samples)]
-            
+
             base, ext = os.path.splitext(os.path.basename(file))
             new_filename = f"{base}_{sufix}{ext}"
-            output_path = os.path.join(
-                output_dir, "analysis_results", new_filename
-            )
+            output_path = os.path.join(output_dir, "analysis_results", new_filename)
             file_df.to_csv(output_path, index=False, sep=extdict.get(file_extension))
             return
 
@@ -771,7 +776,7 @@ def extract_batch_rows_to_file(file, sufix):
             sample_colpos = self.get_sample_idx_colpos(key)
             for file in files:
                 try:
-                    extract_batch_rows_to_file(file,sufix)
+                    extract_batch_rows_to_file(file, sufix)
                 except Exception as e:
                     if self.software_config[key].get("required"):
                         log_type = "error"
@@ -794,17 +799,22 @@ def merge_metadata(self, batch_filepath, batch_data):
             batch_data (dict): A dictionary containing metadata of the samples.
         Returns:
             None
-        """        
+        """
         merged_metadata = relecov_tools.utils.read_json_file(batch_filepath)
-        prev_metadata_dict = {item["sequencing_sample_id"]: item for item in merged_metadata}
+        prev_metadata_dict = {
+            item["sequencing_sample_id"]: item for item in merged_metadata
+        }
         for item in batch_data:
             sample_id = item["sequencing_sample_id"]
             if sample_id in prev_metadata_dict:
                 # When sample already in metadata, checking whether dictionary is the same
                 if prev_metadata_dict[sample_id] != item:
-                    stderr.print(f"[red] Sample {sample_id} has different data in {batch_filepath} and new metadata. Can't merge.")
+                    stderr.print(
+                        f"[red] Sample {sample_id} has different data in {batch_filepath} and new metadata. Can't merge."
+                    )
                     log.error(
-                        "Sample %s has different data in %s and new metadata. Can't merge." % (sample_id, batch_filepath)
+                        "Sample %s has different data in %s and new metadata. Can't merge."
+                        % (sample_id, batch_filepath)
                     )
                     sys.exit(1)
             else:
@@ -842,11 +852,18 @@ def save_splitted_files(self, files_dict, batch_date, output_folder=None):
                     continue
                 try:
                     # Dynamically import the function from the specified module
-                    utils_name = f"relecov_tools.assets.pipeline_utils.{self.software_name}"
+                    utils_name = (
+                        f"relecov_tools.assets.pipeline_utils.{self.software_name}"
+                    )
                     import_statement = f"import {utils_name}"
                     exec(import_statement)
                     # Get method name and execute it.
-                    data = eval(utils_name + "." + func_name + "(file_path, batch_date, output_folder)")
+                    data = eval(
+                        utils_name
+                        + "."
+                        + func_name
+                        + "(file_path, batch_date, output_folder)"
+                    )
                 except Exception as e:
                     self.log_report.update_log_report(
                         self.save_splitted_files.__name__,
@@ -855,7 +872,7 @@ def save_splitted_files(self, files_dict, batch_date, output_folder=None):
                     )
                     sys.exit(self.log_report.print_log_report(method_name, ["error"]))
         return
-    
+
     def get_multiple_sample_files(self):
         method_name = f"{self.add_bioinfo_files_path.__name__}:{self.get_multiple_sample_files.__name__}"
         multiple_sample_files = []
@@ -880,7 +897,7 @@ def create_bioinfo_file(self):
         # Split files found based on each batch of samples
         data_by_batch = self.split_data_by_batch(self.j_data)
         batch_dates = []
-        #Get batch date for all the samples
+        # Get batch date for all the samples
         for batch_dir, batch_dict in data_by_batch.items():
             if batch_dir.split("/")[-1] not in batch_dates:
                 batch_dates.append(batch_dir.split("/")[-1])
@@ -888,8 +905,12 @@ def create_bioinfo_file(self):
         if len(batch_dates) == 1:
             batch_dates = str(batch_dates[0])
         else:
-            stderr.print(f"[orange]More than one batch date in the same json data. Using current date as batch date.")
-            log.info("]More than one batch date in the same json data. Using current date as batch date.")
+            stderr.print(
+                f"[orange]More than one batch date in the same json data. Using current date as batch date."
+            )
+            log.info(
+                "]More than one batch date in the same json data. Using current date as batch date."
+            )
             batch_dates = datetime.now().strftime("%Y%m%d%H%M%S")
 
         # Add bioinfo metadata to j_data
@@ -917,8 +938,13 @@ def create_bioinfo_file(self):
             batch_filename = tag + lab_code + "_" + batch_date + ".json"
             batch_filepath = os.path.join(batch_dir, batch_filename)
             if os.path.exists(batch_filepath):
-                stderr.print(f"[blue]Bioinfo metadata {batch_filepath} file already exists. Merging new data if possible.")
-                log.info("Bioinfo metadata %s file already exists. Merging new data if possible." % batch_filepath)
+                stderr.print(
+                    f"[blue]Bioinfo metadata {batch_filepath} file already exists. Merging new data if possible."
+                )
+                log.info(
+                    "Bioinfo metadata %s file already exists. Merging new data if possible."
+                    % batch_filepath
+                )
                 batch_data = self.merge_metadata(batch_filepath, batch_data)
             else:
                 relecov_tools.utils.write_json_fo_file(batch_data, batch_filepath)
@@ -941,8 +967,13 @@ def create_bioinfo_file(self):
         stderr.print("[blue]Writting output json file")
         file_path = os.path.join(out_path, batch_filename)
         if os.path.exists(file_path):
-            stderr.print(f"[blue]Bioinfo metadata {file_path} file already exists. Merging new data if possible.")
-            log.info("Bioinfo metadata %s file already exists. Merging new data if possible." % file_path)
+            stderr.print(
+                f"[blue]Bioinfo metadata {file_path} file already exists. Merging new data if possible."
+            )
+            log.info(
+                "Bioinfo metadata %s file already exists. Merging new data if possible."
+                % file_path
+            )
             batch_data = self.merge_metadata(file_path, self.j_data)
         else:
             relecov_tools.utils.write_json_fo_file(self.j_data, file_path)

From b37e8a4063cf454395c092183e90d8b7198ad745 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Mon, 13 Jan 2025 13:39:37 +0100
Subject: [PATCH 12/31] Fixed flake8

---
 relecov_tools/assets/pipeline_utils/viralrecon.py | 3 +--
 relecov_tools/read_bioinfo_metadata.py            | 7 +++----
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/relecov_tools/assets/pipeline_utils/viralrecon.py b/relecov_tools/assets/pipeline_utils/viralrecon.py
index c71009c6..5dbf2d21 100644
--- a/relecov_tools/assets/pipeline_utils/viralrecon.py
+++ b/relecov_tools/assets/pipeline_utils/viralrecon.py
@@ -8,7 +8,6 @@
 import os.path
 
 from pathlib import Path
-from datetime import datetime
 
 import relecov_tools.utils
 from relecov_tools.config_json import ConfigJson
@@ -172,7 +171,7 @@ def save_to_file(self, j_list, batch_date):
                 if sample_name in samples_indict:
                     if samples_indict[sample_name] != item:
                         stderr.print(
-                            f"[red]Same sample has different data in both long tables."
+                            f"[red]Same sample {sample_name} has different data in both long tables."
                         )
                         log.error(
                             "Sample %s has different data in %s and new long table. Can't merge."
diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index 4d3a284e..3c8cad2b 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -871,10 +871,9 @@ def save_splitted_files(self, files_dict, batch_date, output_folder=None):
                         f"Error occurred while parsing '{func_name}': {e}.",
                     )
                     sys.exit(self.log_report.print_log_report(method_name, ["error"]))
-        return
+        return data
 
     def get_multiple_sample_files(self):
-        method_name = f"{self.add_bioinfo_files_path.__name__}:{self.get_multiple_sample_files.__name__}"
         multiple_sample_files = []
         for key in self.software_config.keys():
             if self.software_config[key].get("multiple_samples"):
@@ -906,10 +905,10 @@ def create_bioinfo_file(self):
             batch_dates = str(batch_dates[0])
         else:
             stderr.print(
-                f"[orange]More than one batch date in the same json data. Using current date as batch date."
+                "[orange]More than one batch date in the same json data. Using current date as batch date."
             )
             log.info(
-                "]More than one batch date in the same json data. Using current date as batch date."
+                "More than one batch date in the same json data. Using current date as batch date."
             )
             batch_dates = datetime.now().strftime("%Y%m%d%H%M%S")
 

From 97d944e89f01cfa034cdf29e906e035aff89332c Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Tue, 14 Jan 2025 10:04:53 +0100
Subject: [PATCH 13/31] fixed black

---
 relecov_tools/assets/pipeline_utils/viralrecon.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/relecov_tools/assets/pipeline_utils/viralrecon.py b/relecov_tools/assets/pipeline_utils/viralrecon.py
index 5dbf2d21..b48e7c6b 100644
--- a/relecov_tools/assets/pipeline_utils/viralrecon.py
+++ b/relecov_tools/assets/pipeline_utils/viralrecon.py
@@ -322,9 +322,9 @@ def get_pango_data_version(files_list):
                 )
                 # Add custom content in pangolin
                 pango_data_key = next(iter(pango_data))
-                pango_data[pango_data_key][
-                    "lineage_analysis_date"
-                ] = relecov_tools.utils.get_file_date(pango_file)
+                pango_data[pango_data_key]["lineage_analysis_date"] = (
+                    relecov_tools.utils.get_file_date(pango_file)
+                )
                 pango_data[pango_data_key]["pangolin_database_version"] = pango_data_v
                 # Rename key in f_data
                 pango_data_updated = {

From e10a094c113c1f8ec0ed76a6e07fe20b0bbd3085 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Tue, 14 Jan 2025 10:06:00 +0100
Subject: [PATCH 14/31] added creation of log in batch folder

---
 relecov_tools/read_bioinfo_metadata.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index 3c8cad2b..095f99d5 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -980,4 +980,10 @@ def create_bioinfo_file(self):
         self.log_report.logsum.create_error_summary(
             called_module="read-bioinfo-metadata", logs=self.log_report.logsum.logs
         )
+        for batch_dir, batch_dict in data_by_batch.items():
+            self.log_report.logsum.create_error_summary(
+                called_module="read-bioinfo-metadata",
+                filepath=batch_dir,
+                logs=self.log_report.logsum.logs
+            )
         return True

From 6864e95585b2a0c29522e0a8d68e46f7d6327d5e Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Tue, 14 Jan 2025 15:28:56 +0100
Subject: [PATCH 15/31] fixed regex to find long table in analysis_results

---
 relecov_tools/assets/pipeline_utils/viralrecon.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/relecov_tools/assets/pipeline_utils/viralrecon.py b/relecov_tools/assets/pipeline_utils/viralrecon.py
index b48e7c6b..46546147 100644
--- a/relecov_tools/assets/pipeline_utils/viralrecon.py
+++ b/relecov_tools/assets/pipeline_utils/viralrecon.py
@@ -134,7 +134,7 @@ def convert_to_json(self, samp_dict):
         j_list = []
         # Grab date from filename
         result_regex = re.search(
-            "variants_long_table(?:_\d{8})?\.csv", os.path.basename(self.file_path)
+            "variants_long_table(?:_\d{14})?\.csv", os.path.basename(self.file_path)
         )
         if result_regex is None:
             stderr.print(

From f58e0736bf52030d6c52fe0cfde16ea51b91b5e2 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Tue, 14 Jan 2025 15:29:43 +0100
Subject: [PATCH 16/31] removed log that was not working

---
 relecov_tools/read_bioinfo_metadata.py | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index 095f99d5..3c8cad2b 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -980,10 +980,4 @@ def create_bioinfo_file(self):
         self.log_report.logsum.create_error_summary(
             called_module="read-bioinfo-metadata", logs=self.log_report.logsum.logs
         )
-        for batch_dir, batch_dict in data_by_batch.items():
-            self.log_report.logsum.create_error_summary(
-                called_module="read-bioinfo-metadata",
-                filepath=batch_dir,
-                logs=self.log_report.logsum.logs
-            )
         return True

From 718e66b7e36d147db95acb2e478d9bde58cfce75 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Tue, 14 Jan 2025 15:30:29 +0100
Subject: [PATCH 17/31] split files by batch first

---
 relecov_tools/read_bioinfo_metadata.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index 3c8cad2b..297c7ecf 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -920,6 +920,7 @@ def create_bioinfo_file(self):
             stderr.print(f"[blue]Processing data from {batch_dir}")
             batch_data = batch_dict["j_data"]
             stderr.print("[blue]Adding bioinfo metadata to read lab metadata...")
+            self.split_tables_by_batch(files_found_dict, sufix, batch_data, batch_dir)
             batch_data = self.add_bioinfo_results_metadata(
                 files_found_dict, batch_data, batch_date, batch_dir
             )
@@ -932,7 +933,6 @@ def create_bioinfo_file(self):
             # Adding files path
             stderr.print("[blue]Adding files path to read lab metadata")
             batch_data = self.add_bioinfo_files_path(files_found_dict, batch_data)
-            self.split_tables_by_batch(files_found_dict, batch_data, batch_dir)
             tag = "bioinfo_lab_metadata_"
             batch_filename = tag + lab_code + "_" + batch_date + ".json"
             batch_filepath = os.path.join(batch_dir, batch_filename)

From 72c76b3ca4c960a1c489a4e63cdc17ea8a554ae3 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Tue, 14 Jan 2025 15:31:57 +0100
Subject: [PATCH 18/31] created unique sufix for all files in batch

---
 relecov_tools/read_bioinfo_metadata.py | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index 297c7ecf..9a659f8d 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -234,7 +234,7 @@ def validate_software_mandatory_files(self, files_dict):
         return
 
     def add_bioinfo_results_metadata(
-        self, files_dict, j_data, batch_id, output_folder=None
+        self, files_dict, j_data, sufix, batch_id, output_folder=None
     ):
         """Adds metadata from bioinformatics results to j_data.
         It first calls file_handlers and then maps the handled
@@ -243,6 +243,7 @@ def add_bioinfo_results_metadata(
         Args:
             files_dict (dict{str:str}): A dictionary containing file paths found based on the definitions provided in the bioinformatic JSON file within the software scope (self.software_config).
             j_data (list(dict{str:str}): A list of dictionaries containing metadata lab (list item per sample).
+            sufix (str): Sufix added to splitted tables file name.
             output_folder (str): Path to save output files generated during handling_files() process.
             batch_id(str): ID of the batch which corresponds with the data download date.
 
@@ -267,7 +268,7 @@ def add_bioinfo_results_metadata(
                 )
                 continue
             # Handling files
-            data_to_map = self.handling_files(files_dict[key], output_folder, batch_id)
+            data_to_map = self.handling_files(files_dict[key], sufix, output_folder, batch_id)
             # Mapping data to j_data
             mapping_fields = self.software_config[key].get("content")
             if not mapping_fields:
@@ -328,7 +329,7 @@ def handling_tables(self, file_list, conf_tab_name):
             sys.exit(self.log_report.print_log_report(method_name, ["error"]))
         return data
 
-    def handling_files(self, file_list, output_folder, batch_id):
+    def handling_files(self, file_list, sufix, output_folder, batch_id):
         """Handles different file formats to extract data regardless of their structure.
         The goal is to extract the data contained in files specified in ${file_list},
         using either 'standard' handlers defined in this class or pipeline-specific file handlers.
@@ -739,11 +740,12 @@ def split_data_by_batch(self, j_data):
             ]
         return data_by_batch
 
-    def split_tables_by_batch(self, files_found_dict, batch_data, output_dir):
+    def split_tables_by_batch(self, files_found_dict, sufix, batch_data, output_dir):
         """Filter table content to output a new table containing only the samples present in given metadata
 
         Args:
             files_found_dict (dict): A dictionary containing file paths identified for each configuration item.
+            sufix (str): Sufix to be added to the new table file name.
             batch_data (list(dict)): Metadata corresponding to a single folder with samples (folder)
             output_dir (str): Output location for the generated tabular file
         """
@@ -767,7 +769,6 @@ def extract_batch_rows_to_file(file, sufix):
 
         method_name = self.split_tables_by_batch.__name__
         namekey = "sequencing_sample_id"
-        sufix = datetime.now().strftime("%Y%m%d%H%M%S")
         batch_samples = [row.get(namekey) for row in batch_data]
         for key, files in files_found_dict.items():
             if not self.software_config[key].get("split_by_batch"):
@@ -896,6 +897,7 @@ def create_bioinfo_file(self):
         # Split files found based on each batch of samples
         data_by_batch = self.split_data_by_batch(self.j_data)
         batch_dates = []
+        sufix = datetime.now().strftime("%Y%m%d%H%M%S")
         # Get batch date for all the samples
         for batch_dir, batch_dict in data_by_batch.items():
             if batch_dir.split("/")[-1] not in batch_dates:
@@ -922,7 +924,7 @@ def create_bioinfo_file(self):
             stderr.print("[blue]Adding bioinfo metadata to read lab metadata...")
             self.split_tables_by_batch(files_found_dict, sufix, batch_data, batch_dir)
             batch_data = self.add_bioinfo_results_metadata(
-                files_found_dict, batch_data, batch_date, batch_dir
+                files_found_dict, batch_data, sufix, batch_date, batch_dir
             )
             stderr.print("[blue]Adding software versions to read lab metadata...")
             batch_data = self.get_multiqc_software_versions(

From 68f6b983487c75d4a99f7a0cfb435c93dfa2b75e Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Tue, 14 Jan 2025 15:32:31 +0100
Subject: [PATCH 19/31] renamed save_splitted_files to save_merged_files

---
 relecov_tools/read_bioinfo_metadata.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index 9a659f8d..d4061548 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -824,9 +824,9 @@ def merge_metadata(self, batch_filepath, batch_data):
         relecov_tools.utils.write_json_fo_file(merged_metadata, batch_filepath)
         return merged_metadata
 
-    def save_splitted_files(self, files_dict, batch_date, output_folder=None):
+    def save_merged_files(self, files_dict, batch_date, output_folder=None):
         """
-        Process and save files that where split by batch and that have a function to be processed
+        Process and save files that where split by cod and that have a function to be processed
 
         Args:
             files_dict (dict): A dictionary containing file paths identified for each configuration item.
@@ -836,7 +836,7 @@ def save_splitted_files(self, files_dict, batch_date, output_folder=None):
         Returns:
             None
         """
-        method_name = f"{self.save_splitted_files.__name__}"
+        method_name = f"{self.save_merged_files.__name__}"
         for key, config in self.software_config.items():
             func_name = config.get("function")
             # Skip configurations that do not match the conditions
@@ -867,7 +867,7 @@ def save_splitted_files(self, files_dict, batch_date, output_folder=None):
                     )
                 except Exception as e:
                     self.log_report.update_log_report(
-                        self.save_splitted_files.__name__,
+                        self.save_merged_files.__name__,
                         "error",
                         f"Error occurred while parsing '{func_name}': {e}.",
                     )
@@ -963,7 +963,7 @@ def create_bioinfo_file(self):
         tag = "bioinfo_lab_metadata_"
         stderr.print("[blue]Saving previously splitted files to output directory")
 
-        self.save_splitted_files(files_found_dict, batch_dates, out_path)
+        self.save_merged_files(files_found_dict, batch_dates, out_path)
         batch_filename = tag + batch_dates + ".json"
         stderr.print("[blue]Writting output json file")
         file_path = os.path.join(out_path, batch_filename)

From 0d82573148860e159673265e9492e4472e01c389 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Tue, 14 Jan 2025 15:33:00 +0100
Subject: [PATCH 20/31] added code to save splitted long table to batch dir

---
 relecov_tools/read_bioinfo_metadata.py | 73 +++++++++++++++++++-------
 1 file changed, 53 insertions(+), 20 deletions(-)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index d4061548..9a9720f2 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -361,31 +361,64 @@ def handling_files(self, file_list, sufix, output_folder, batch_id):
             data: A dictionary containing bioinfo metadata handled for each sample.
         """
         method_name = f"{self.add_bioinfo_results_metadata.__name__}:{self.handling_files.__name__}"
+        splitted_path = os.path.join(output_folder, "analysis_results")
         file_name = self.software_config[self.current_config_key].get("fn")
         # Parsing files
-        func_name = self.software_config[self.current_config_key]["function"]
+        current_config = self.software_config[self.current_config_key]
+        func_name = current_config.get("function")
         if func_name is None:
             data = self.handling_tables(file_list=file_list, conf_tab_name=file_name)
         else:
-            try:
-                # Dynamically import the function from the specified module
-                utils_name = f"relecov_tools.assets.pipeline_utils.{self.software_name}"
-                import_statement = f"import {utils_name}"
-                exec(import_statement)
-                # Get method name and execute it.
-                data = eval(
-                    utils_name
-                    + "."
-                    + func_name
-                    + "(file_list, batch_id, output_folder)"
-                )
-            except Exception as e:
-                self.log_report.update_log_report(
-                    self.add_bioinfo_results_metadata.__name__,
-                    "error",
-                    f"Error occurred while parsing '{func_name}': {e}.",
-                )
-                sys.exit(self.log_report.print_log_report(method_name, ["error"]))
+            if current_config.get("split_by_batch") is True:
+                file_extension = current_config.get("fn").rsplit(".", 1)[1]
+                base_filename = current_config.get("fn").rsplit(".", 1)[0]
+                pattern = re.compile(f"{base_filename}_{sufix}.{re.escape(file_extension)}")
+                matching_files = [
+                    f for f in os.listdir(splitted_path) if pattern.match(f)
+                ]
+                full_paths = [os.path.join(splitted_path, f) for f in matching_files]
+                try:
+                    # Dynamically import the function from the specified module
+                    utils_name = (
+                        f"relecov_tools.assets.pipeline_utils.{self.software_name}"
+                    )
+                    import_statement = f"import {utils_name}"
+                    exec(import_statement)
+                    # Get method name and execute it.
+                    print("lanzar_variants_long_table")
+                    data = eval(
+                        utils_name
+                        + "."
+                        + func_name
+                        + "(full_paths, batch_id, output_folder)"
+                    )
+                except Exception as e:
+                    self.log_report.update_log_report(
+                        self.save_splitted_files.__name__,
+                        "error",
+                        f"Error occurred while parsing '{func_name}': {e}.",
+                    )
+                    sys.exit(self.log_report.print_log_report(method_name, ["error"]))
+            else:
+                try:
+                    # Dynamically import the function from the specified module
+                    utils_name = f"relecov_tools.assets.pipeline_utils.{self.software_name}"
+                    import_statement = f"import {utils_name}"
+                    exec(import_statement)
+                    # Get method name and execute it.
+                    data = eval(
+                        utils_name
+                        + "."
+                        + func_name
+                        + "(file_list, batch_id, output_folder)"
+                    )
+                except Exception as e:
+                    self.log_report.update_log_report(
+                        self.add_bioinfo_results_metadata.__name__,
+                        "error",
+                        f"Error occurred while parsing '{func_name}': {e}.",
+                    )
+                    sys.exit(self.log_report.print_log_report(method_name, ["error"]))
         return data
 
     def mapping_over_table(self, j_data, map_data, mapping_fields, table_name):

From 09b58dad41d84a69966dbf625cfb9192046b47a8 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Tue, 14 Jan 2025 15:33:49 +0100
Subject: [PATCH 21/31] fixed black

---
 relecov_tools/read_bioinfo_metadata.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index 9a9720f2..69b045cd 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -268,7 +268,9 @@ def add_bioinfo_results_metadata(
                 )
                 continue
             # Handling files
-            data_to_map = self.handling_files(files_dict[key], sufix, output_folder, batch_id)
+            data_to_map = self.handling_files(
+                files_dict[key], sufix, output_folder, batch_id
+            )
             # Mapping data to j_data
             mapping_fields = self.software_config[key].get("content")
             if not mapping_fields:
@@ -372,7 +374,9 @@ def handling_files(self, file_list, sufix, output_folder, batch_id):
             if current_config.get("split_by_batch") is True:
                 file_extension = current_config.get("fn").rsplit(".", 1)[1]
                 base_filename = current_config.get("fn").rsplit(".", 1)[0]
-                pattern = re.compile(f"{base_filename}_{sufix}.{re.escape(file_extension)}")
+                pattern = re.compile(
+                    f"{base_filename}_{sufix}.{re.escape(file_extension)}"
+                )
                 matching_files = [
                     f for f in os.listdir(splitted_path) if pattern.match(f)
                 ]
@@ -402,7 +406,9 @@ def handling_files(self, file_list, sufix, output_folder, batch_id):
             else:
                 try:
                     # Dynamically import the function from the specified module
-                    utils_name = f"relecov_tools.assets.pipeline_utils.{self.software_name}"
+                    utils_name = (
+                        f"relecov_tools.assets.pipeline_utils.{self.software_name}"
+                    )
                     import_statement = f"import {utils_name}"
                     exec(import_statement)
                     # Get method name and execute it.

From f08c12a88a53a1985cb13e0e60f01eb7651d5b99 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Tue, 14 Jan 2025 15:44:18 +0100
Subject: [PATCH 22/31] added log errors

---
 relecov_tools/assets/pipeline_utils/viralrecon.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/relecov_tools/assets/pipeline_utils/viralrecon.py b/relecov_tools/assets/pipeline_utils/viralrecon.py
index 46546147..7ec18895 100644
--- a/relecov_tools/assets/pipeline_utils/viralrecon.py
+++ b/relecov_tools/assets/pipeline_utils/viralrecon.py
@@ -188,7 +188,7 @@ def save_to_file(self, j_list, batch_date):
                 )
             except Exception as e:
                 stderr.print("[red]\tError saving parsed data to file:", str(e))
-
+                log.error("Error saving parsed data to file: %s", e)
         else:
             try:
                 with open(file_path, "w") as fh:
@@ -198,6 +198,7 @@ def save_to_file(self, j_list, batch_date):
                 )
             except Exception as e:
                 stderr.print("[red]\tError saving parsed data to file:", str(e))
+                log.error("Error saving parsed data to file: %s", e)
 
     def parsing_csv(self):
         """

From d09ca2617e85a4fc19d5d3925ca2e19038feee92 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Tue, 14 Jan 2025 15:45:07 +0100
Subject: [PATCH 23/31] replaced batch_id with batch_date

---
 relecov_tools/assets/pipeline_utils/viralrecon.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/relecov_tools/assets/pipeline_utils/viralrecon.py b/relecov_tools/assets/pipeline_utils/viralrecon.py
index 7ec18895..9613ffa8 100644
--- a/relecov_tools/assets/pipeline_utils/viralrecon.py
+++ b/relecov_tools/assets/pipeline_utils/viralrecon.py
@@ -354,7 +354,7 @@ def get_pango_data_version(files_list):
     return pango_data_processed
 
 
-def parse_long_table(files_list, batch_id, output_folder=None):
+def parse_long_table(files_list, batch_date, output_folder=None):
     """File handler to retrieve data from long table files and convert it into a JSON structured format.
     This function utilizes the LongTableParse class to parse the long table data.
     Since this utility handles and maps data using a custom way, it returns None to be avoid being  transferred to method read_bioinfo_metadata.BioinfoMetadata.mapping_over_table().
@@ -383,7 +383,7 @@ def parse_long_table(files_list, batch_id, output_folder=None):
         # Parsing long table data and saving it
         long_table_data = long_table.parsing_csv()
         # Saving long table data into a file
-        long_table.save_to_file(long_table_data, batch_id)
+        long_table.save_to_file(long_table_data, batch_date)
         stderr.print("[green]\tProcess completed")
     elif len(files_list) > 1:
         method_log_report.update_log_report(
@@ -395,7 +395,7 @@ def parse_long_table(files_list, batch_id, output_folder=None):
     return None
 
 
-def handle_consensus_fasta(files_list, batch_id, output_folder=None):
+def handle_consensus_fasta(files_list, batch_date, output_folder=None):
     """File handler to parse consensus data (fasta) into JSON structured format.
 
     Args:

From 55bd6117351daff59d071614b571b2f89f4824cc Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Tue, 14 Jan 2025 15:46:59 +0100
Subject: [PATCH 24/31] replaced batch_id with batch_date

---
 relecov_tools/read_bioinfo_metadata.py | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index 69b045cd..a02a9e18 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -234,7 +234,7 @@ def validate_software_mandatory_files(self, files_dict):
         return
 
     def add_bioinfo_results_metadata(
-        self, files_dict, j_data, sufix, batch_id, output_folder=None
+        self, files_dict, j_data, sufix, batch_date, output_folder=None
     ):
         """Adds metadata from bioinformatics results to j_data.
         It first calls file_handlers and then maps the handled
@@ -245,7 +245,7 @@ def add_bioinfo_results_metadata(
             j_data (list(dict{str:str}): A list of dictionaries containing metadata lab (list item per sample).
             sufix (str): Sufix added to splitted tables file name.
             output_folder (str): Path to save output files generated during handling_files() process.
-            batch_id(str): ID of the batch which corresponds with the data download date.
+            batch_date(str): Number of the batch which corresponds with the data download date.
 
         Returns:
             j_data_mapped: A list of dictionaries with bioinformatics metadata mapped into j_data.
@@ -269,7 +269,7 @@ def add_bioinfo_results_metadata(
                 continue
             # Handling files
             data_to_map = self.handling_files(
-                files_dict[key], sufix, output_folder, batch_id
+                files_dict[key], sufix, output_folder, batch_date
             )
             # Mapping data to j_data
             mapping_fields = self.software_config[key].get("content")
@@ -331,7 +331,7 @@ def handling_tables(self, file_list, conf_tab_name):
             sys.exit(self.log_report.print_log_report(method_name, ["error"]))
         return data
 
-    def handling_files(self, file_list, sufix, output_folder, batch_id):
+    def handling_files(self, file_list, sufix, output_folder, batch_date):
         """Handles different file formats to extract data regardless of their structure.
         The goal is to extract the data contained in files specified in ${file_list},
         using either 'standard' handlers defined in this class or pipeline-specific file handlers.
@@ -358,6 +358,7 @@ def handling_files(self, file_list, sufix, output_folder, batch_id):
         Args:
             file_list (list): A list of file path/s to be processed.
             output_folder (str): Path to save output files from imported method if necessary
+            batch_date(str): Number of the batch which corresponds with the data download date.
 
         Returns:
             data: A dictionary containing bioinfo metadata handled for each sample.
@@ -394,7 +395,7 @@ def handling_files(self, file_list, sufix, output_folder, batch_id):
                         utils_name
                         + "."
                         + func_name
-                        + "(full_paths, batch_id, output_folder)"
+                        + "(full_paths, batch_date, output_folder)"
                     )
                 except Exception as e:
                     self.log_report.update_log_report(
@@ -416,7 +417,7 @@ def handling_files(self, file_list, sufix, output_folder, batch_id):
                         utils_name
                         + "."
                         + func_name
-                        + "(file_list, batch_id, output_folder)"
+                        + "(file_list, batch_date, output_folder)"
                     )
                 except Exception as e:
                     self.log_report.update_log_report(

From a480315d6ad57a8c0758ab6da634b776f051ee5e Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Tue, 14 Jan 2025 15:50:06 +0100
Subject: [PATCH 25/31] Updated changelog

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 753732a2..262eb0f0 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,6 +22,8 @@ Code contributions to the release:
 
 #### Fixes
 
+- Fixed read-bioinfo-metadata module [#367](https://github.com/BU-ISCIII/relecov-tools/pull/367)
+
 #### Changed
 
 #### Removed

From d6cd9beadde79c4f1b80cb53fbc91bfef53daf36 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Wed, 15 Jan 2025 14:41:08 +0100
Subject: [PATCH 26/31] Added creation of analysis_results earlier for module
 to work

---
 relecov_tools/read_bioinfo_metadata.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index a02a9e18..429ae414 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -803,6 +803,7 @@ def extract_batch_rows_to_file(file, sufix):
 
             base, ext = os.path.splitext(os.path.basename(file))
             new_filename = f"{base}_{sufix}{ext}"
+            os.makedirs(os.path.join(output_dir, "analysis_results"), exist_ok=True)
             output_path = os.path.join(output_dir, "analysis_results", new_filename)
             file_df.to_csv(output_path, index=False, sep=extdict.get(file_extension))
             return

From 2af25d7abb54f82fa1feb4fb0b149fe6ca50439f Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Wed, 15 Jan 2025 16:33:13 +0100
Subject: [PATCH 27/31] ignored flake error

---
 relecov_tools/read_bioinfo_metadata.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index 429ae414..4ac782b7 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -381,7 +381,7 @@ def handling_files(self, file_list, sufix, output_folder, batch_date):
                 matching_files = [
                     f for f in os.listdir(splitted_path) if pattern.match(f)
                 ]
-                full_paths = [os.path.join(splitted_path, f) for f in matching_files]
+                full_paths = [os.path.join(splitted_path, f) for f in matching_files] # noqua: F841
                 try:
                     # Dynamically import the function from the specified module
                     utils_name = (

From a68a3ebebdf382b749acbacafa4500946fd512bf Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Wed, 15 Jan 2025 16:34:35 +0100
Subject: [PATCH 28/31] flixed black and flake

---
 relecov_tools/read_bioinfo_metadata.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index 4ac782b7..b070c656 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -381,7 +381,7 @@ def handling_files(self, file_list, sufix, output_folder, batch_date):
                 matching_files = [
                     f for f in os.listdir(splitted_path) if pattern.match(f)
                 ]
-                full_paths = [os.path.join(splitted_path, f) for f in matching_files] # noqua: F841
+                full_paths = [os.path.join(splitted_path, f) for f in matching_files]  # noqua: F841
                 try:
                     # Dynamically import the function from the specified module
                     utils_name = (

From 97be5731d83121081792cfce51e8bfd2089b689b Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Wed, 15 Jan 2025 16:36:33 +0100
Subject: [PATCH 29/31] fixed black and flake

---
 relecov_tools/read_bioinfo_metadata.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index b070c656..a7fdc39f 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -381,7 +381,9 @@ def handling_files(self, file_list, sufix, output_folder, batch_date):
                 matching_files = [
                     f for f in os.listdir(splitted_path) if pattern.match(f)
                 ]
-                full_paths = [os.path.join(splitted_path, f) for f in matching_files]  # noqua: F841
+                full_paths = [
+                    os.path.join(splitted_path, f) for f in matching_files
+                ]  # noqa: F841
                 try:
                     # Dynamically import the function from the specified module
                     utils_name = (

From 6c2556e1770da57ea5cbe5117fdec5bcb237c8ee Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Wed, 15 Jan 2025 16:39:33 +0100
Subject: [PATCH 30/31] finally fixed flake8

---
 relecov_tools/read_bioinfo_metadata.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index a7fdc39f..db5d98f8 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -381,9 +381,9 @@ def handling_files(self, file_list, sufix, output_folder, batch_date):
                 matching_files = [
                     f for f in os.listdir(splitted_path) if pattern.match(f)
                 ]
-                full_paths = [
+                full_paths = [  # noqa: F841
                     os.path.join(splitted_path, f) for f in matching_files
-                ]  # noqa: F841
+                ]
                 try:
                     # Dynamically import the function from the specified module
                     utils_name = (

From e90d33db27821b285e67c8bda7df8995db7382f3 Mon Sep 17 00:00:00 2001
From: svarona <sarai.var.fer@gmail.com>
Date: Wed, 15 Jan 2025 16:50:53 +0100
Subject: [PATCH 31/31] removed print

---
 relecov_tools/read_bioinfo_metadata.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/relecov_tools/read_bioinfo_metadata.py b/relecov_tools/read_bioinfo_metadata.py
index db5d98f8..0e0d8020 100755
--- a/relecov_tools/read_bioinfo_metadata.py
+++ b/relecov_tools/read_bioinfo_metadata.py
@@ -392,7 +392,6 @@ def handling_files(self, file_list, sufix, output_folder, batch_date):
                     import_statement = f"import {utils_name}"
                     exec(import_statement)
                     # Get method name and execute it.
-                    print("lanzar_variants_long_table")
                     data = eval(
                         utils_name
                         + "."