fix: sample sheet processing and run id searching fixes from bigsky testing

Author: rroutsong

scripts/files.py

@@ -155,6 +155,10 @@ def get_run_directories(runids, seq_dir=None, sheetname=None):
     host = get_current_server()
     seq_dirs = Path(seq_dir).absolute() if seq_dir else Path(DIRECTORY_CONFIGS[host]['seqroot'])
     seq_contents = [_child for _child in seq_dirs.iterdir()]
+    for firstchild in seq_dirs.iterdir():
+        if firstchild.is_dir():
+            for secondchild in firstchild.iterdir():
+                seq_contents.append(secondchild)
     seq_contents_names = [child for child in map(lambda d: d.name, seq_contents)]
 
     run_paths, invalid_runs  = [], []

scripts/samplesheet.py

@@ -65,13 +65,16 @@ def parse_sheet(self, sheet):
     def process_v1_reads_section(self, section):
         section = [x for x in section if set(x) != {','}]
         r1, r2 = None, None
-        for i, line in enumerate(section, start=1):
-            if line.split(',')[0].isnumeric() and i == 1:
-                r1 = int(line.split(',')[0])
-            elif line.split(',')[0].isnumeric() and i == 2:
-                r2 = int(line.split(',')[0])
-            else:
-                self.process_simple_section([line])        
+        for line in section:
+            this_line_name = line.split(',')[0]
+            this_line_val = line.split(',')[1]
+            if this_line_name.lower() in ('read01', 'read02') and this_line_val.isnumeric():
+                if this_line_name.endswith('1') and int(this_line_val) > 0:
+                    r1 = int(this_line_val)
+                elif this_line_name.endswith('2') and int(this_line_val) > 0:
+                    r2 = int(this_line_val)
+        else:
+            self.process_simple_section([line])
         if r1:
             setattr(self, 'Read01', r1)
         if r2: