🌙 🚲

BRB/PushButton.py

@@ -8,7 +8,7 @@
 import stat
 from pathlib import Path
 
-def createPath(config, group, project, organism, libraryType, tuples):
+def createPath(config, group, project, organism, libraryType, tuples, stats):
     """Ensures that the output path exists, creates it otherwise, and return where it is"""
     if tuples[0][3]:
         baseDir = "{}/{}/Analysis_{}".format(config.get('Paths', 'baseData'),
@@ -20,10 +20,14 @@ def createPath(config, group, project, organism, libraryType, tuples):
                                                             BRB.misc.getLatestSeqdir(config.get('Paths','groupData'), group),
                                                             config.get('Options', 'runID'),
                                                             BRB.misc.pacifier(project))
-    os.makedirs(baseDir, mode=0o700, exist_ok=True)
+
+    if not stats:
+        os.makedirs(baseDir, mode=0o700, exist_ok=True)
 
     oDir = os.path.join(baseDir, "{}_{}".format(BRB.misc.pacifier(libraryType), organism.split(' ')[0].lower()))
-    os.makedirs(oDir, mode=0o700, exist_ok=True)
+    if not stats:
+        os.makedirs(oDir, mode=0o700, exist_ok=True)
+
     return oDir
 
 
@@ -564,7 +568,7 @@ def scATAC(config, group, project, organism, libraryType, tuples):
     return outputDir, 0, True
 
 
-def GetResults(config, project, libraries):
+def GetResults(config, project, libraries, stats):
     """
     Project is something like '352_Grzes_PearceEd' and libraries is a dictionary with libraries as keys:
         {'18L005489': ['FAT_first_A',
@@ -638,7 +642,12 @@ def GetResults(config, project, libraries):
                 reruncount = 0
                 # RELACS needs the unpacified project name to copy the original sample sheet to the dest dir
                 # hence the pacifier is applied on the project in each pipeline separately
-                outputDir, rv, sambaUpdate = globals()[pipeline](config, group, project, organism, libraryType, tuples)
+                if stats:
+                    outputDir, rv, sambaUpdate = (
+                        createPath(config, group, BRB.misc.pacifier(project), organism, libraryType, tuples, stats),
+                        0, False)
+                else:
+                    outputDir, rv, sambaUpdate = globals()[pipeline](config, group, project, organism, libraryType, tuples)
                 if reruncount == 0 and rv != 0:
                     # Allow for one re-run
                     reruncount += 1

BRB/run.py

@@ -15,15 +15,15 @@
 from rich import print
 
 
-def process_data(config, ParkourDict):
+def process_data(config, ParkourDict, stats):
     bdir = "{}/{}".format(config.get('Paths', 'baseData'), config.get('Options', 'runID'))
     msg = []
     for k, v in ParkourDict.items():
         if not os.path.exists("{}/Project_{}".format(bdir, BRB.misc.pacifier(k))):
             log.info("{}/Project_{} doesn't exist, probably lives on another lane.".format(bdir, BRB.misc.pacifier(k)))
             continue
         try:
-            msg = msg + BRB.PushButton.GetResults(config, k, v)
+            msg = msg + BRB.PushButton.GetResults(config, k, v, stats)
         except Exception as e:
             BRB.email.errorEmail(config, sys.exc_info(), "Received an error running PushButton.GetResults() with {} and {}".format(k, v))
             log.critical("Received an error running PushButton.GetResults() with {} and {}".format(k, v))
@@ -116,10 +116,10 @@ def run_brb(configfile, stats, fcid):
             log.info(f"Pushing stats for flowcell: {fcid}")
 
         # Process each group's data, ignore cases where the project isn't in the lanes being processed
-        process_data(config, ParkourDict)
+        process_data(config, ParkourDict, stats)
 
         if stats and dual_lane:
-            process_data(config1, ParkourDict1)
+            process_data(config1, ParkourDict1, stats)
 
 
         if not stats: