Sample ID is now used as the column names in outputs

bin/report_summaries.py

@@ -65,7 +65,6 @@ def write_table(self, table_data: Dict[str, Dict[str, str]]):
         """
         keys = set([k for k in table_data])
         ordered_keys = []
-
         # Get the wanted information to the top of the page
         poisoned_keys = set()
         for option in self.__key_order:
@@ -80,7 +79,6 @@ def write_table(self, table_data: Dict[str, Dict[str, str]]):
         ordered_keys.extend(scalar_keys)
         ordered_keys.extend(sorted([i for i in keys if i not in ordered_keys and i not in poisoned_keys]))
         row_labels = sorted([i for i in next(iter(table_data.values()))])
-
         self.write_tsv(table_data, row_labels, ordered_keys)
         self.write_transposed_tsv(table_data, row_labels, ordered_keys)
 
@@ -135,6 +133,29 @@ def update_table_labels(self, table, keys, info: CleaningInfo):
                 del table[previous]
         return sorted(processed_keys), poisoned_keys
 
+    def key_saver(self, sample_name, keys):
+        """
+        As we split on the period delimiter, and periods are allowed in
+        sample names, some special care needs to be considered in splitting
+        the sample names as to not accidentally drop characters in the names.
+
+        sample_name str: The sample name to be saved from the split string
+        keys list[str]: List of keys to split
+        """
+        return_values = []
+        for k in keys:
+            if k.startswith(sample_name):
+                sample_name_len = len(sample_name)
+                if sample_name.endswith(self.__key_delimiter):
+                    # Need to remove the next delimiter as well if the sample
+                    # ends with one. Or else we end up with an empty string inserted
+                    sample_name_len += 1
+                split_string = k[sample_name_len:]
+                sample_keys = [sample_name, *[i for i in split_string.split(self.__key_delimiter)]]
+                return_values.append(sample_keys)
+                continue
+            return_values.append(k.split(self.__key_delimiter))
+        return return_values
 
     def make_table(self, data):
         """Create an aggregated table of report data from mikrokondo
@@ -146,7 +167,7 @@ def make_table(self, data):
 
         sample_data = defaultdict(list)
         for k, v in data.items():
-            keys = [i.split(self.__key_delimiter) for i in v.keys()]
+            keys = self.key_saver(k, v.keys())
             copy_keys = []
             tool_keys = set()
             for i in keys:
@@ -266,11 +287,11 @@ def output_indv_json(self, flattened_data):
         for k, v in flattened_data.items():
             out_key = k
             sample_dir = k
-            if dir_name := v.get(self.__inx_irida_key) != k:
+            dir_name = v.get(self.__inx_irida_key)
+            if k != dir_name:
                 sample_dir = dir_name
                 #! this field affects the identification of the irida next id being passed out of the pipeline
                 out_key = sample_dir # this field must be overwritten for iridanext to identify the correct metdata field
-
             out_dir = os.path.join(self.output_dir, sample_dir)
             out_path = os.path.join(out_dir, k + self.flat_sample_string)
             if not os.path.isdir(out_dir): # Check for directory existence, as it will still exist on pipeline resumes
@@ -298,7 +319,6 @@ def to_file(self):
                         out_file.write(f'"{val_write}"')
                     else:
                         out_file.write(val_write)
-                        # out_file.write(str(ii[1][i]).replace('\n', ' \\'))
                     out_file.write(self.__delimiter)
                 out_file.write("\n")
 

modules/local/report.nf

@@ -47,6 +47,7 @@ process REPORT{
         }
 
         update_map_values(sample_data, meta_data, "metagenomic")
+        update_map_values(sample_data, meta_data, "id")
         update_map_values(sample_data, meta_data, "sample")
         update_map_values(sample_data, meta_data, "external_id")
         update_map_values(sample_data, meta_data, "assembly")
@@ -55,8 +56,8 @@ process REPORT{
         update_map_values(sample_data, meta_data, "merge")
         update_map_values(sample_data, meta_data, "downsampled")
 
-        if(!sample_data[meta_data.sample].containsKey(meta_data.external_id)){
-            sample_data[meta_data.sample][meta_data.external_id] = [:]
+        if(!sample_data[meta_data.sample].containsKey(meta_data.id)){
+            sample_data[meta_data.sample][meta_data.id] = [:]
         }
 
         if(report_value instanceof Path){
@@ -70,7 +71,7 @@ process REPORT{
             }
         }
 
-        sample_data[meta_data.sample][meta_data.external_id][report_tag.report_tag] = report_value
+        sample_data[meta_data.sample][meta_data.id][report_tag.report_tag] = report_value
     }
 
 

subworkflows/local/input_check.nf

@@ -29,7 +29,7 @@ workflow INPUT_CHECK {
                 // hidden files causing odd issues later on in the pipeline
 
                 if(meta[0].id == null){
-                    // Remove any unallowed charactars in the meta.id field
+                    // Remove any unallowed characters in the meta.id field
                     meta[0].id = meta[0].external_id.replaceAll(/^\./, '_')
                     meta[0].id = meta[0].id.replaceAll(/[^A-Za-z0-9_\.\-]/, '_')
                 }else {
@@ -133,7 +133,8 @@ def format_reads(ArrayList sheet_data){
     def meta = [:]
     def error_occured = false
     meta.id = sheet_data[0] // id is first value
-    meta.sample = sheet_data[1].external_id
+    //meta.sample = sheet_data[1].external_id
+    meta.sample = sheet_data[0]
     meta.external_id = sheet_data[1].external_id
 
     meta.hybrid = false