Main (#159)

maxplanck-ie · Aug 4, 2023 · e181c4e · e181c4e
2 parents e2faafe + 5514b2b
commit e181c4e
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Showing 4 changed files with 46 additions and 8 deletions.
diff --git a/src/dissectBCL/classes.py b/src/dissectBCL/classes.py
@@ -258,9 +258,15 @@ def parseSS(self, parkourDF):
         # ssdf = ssdf.dropna(axis=1, how='all')
 
         ssdf = ssdf.astype({'Lane': 'int32'})
-        # Remove spaces if we have them
-        sp_clean = ssdf['Sample_Project'].apply(lambda x: umlautDestroyer(x))
-        ssdf['Sample_Project'] = sp_clean
+        # Sanitize projects names
+        ssdf['Sample_Project'] = ssdf['Sample_Project'].apply(
+            lambda x: umlautDestroyer(x)
+        )
+        # Sanitize sample names
+        ssdf['Sample_Name'] = ssdf['Sample_Name'].apply(
+            lambda x: umlautDestroyer(x)
+        )
+
         self.fullSS = ssdf
         self.laneSplitStatus = self.decideSplit()
         ssDic = {}
@@ -280,6 +286,26 @@ def parseSS(self, parkourDF):
                             'Sample_Project',
                         ]
                     )
+                    if '-' in self.flowcell:
+                        '''
+                        In case of miSeq runs,
+                        assume the requested depth is 20/#samples
+                        this is due to the 10M / sample
+                        minimum for parkour requests
+                        we do this here (and not in pullparkour)
+                        since parkour returns all
+                        samples, not necesarily those sequenced.
+                        '''
+                        newReqDepth = 20/len(
+                            list(mergeDF['Sample_Name'].unique())
+                        ) * 1000000
+                        newReqDepth = round(newReqDepth, 0)
+                        mergeDF['reqDepth'] = newReqDepth
+                        logging.debug(
+                            'miSEQ detected, override seqdepth: {}'.format(
+                                newReqDepth
+                            )
+                        )
                     ssDic[key] = {'sampleSheet': mergeDF, 'lane': lane}
                 else:
                     ssDic[key] = {

diff --git a/src/dissectBCL/dissect.py b/src/dissectBCL/dissect.py
@@ -70,12 +70,23 @@ def main(config):
                 filemode='a',
                 force=True
             )
-
+            # Set flowcellname in log.
             logging.info("Log Initiated - flowcell:{}, filename:{}".format(
                 flowcellName,
                 logFile
             ))
-
+            # Include dissectBCL version in log
+            logging.info("dissectBCL - version {}".format(
+                version("dissectBCL")
+            ))
+            # Include software versions in log
+            for lib in config['softwareVers']:
+                logging.debug(
+                    "{} = {}".format(
+                        lib,
+                        config['softwareVers'][lib]
+                    )
+                )
             # Create classes.
             flowcell = flowCellClass(
                 name=flowcellName,

diff --git a/src/dissectBCL/fakeNews.py b/src/dissectBCL/fakeNews.py
@@ -93,6 +93,10 @@ def pullParkour(flowcellID, config):
                 'indexType',
                 'reqDepth'
             ]
+        # Sanitize sample names.
+        parkourDF['Sample_Name'] = parkourDF['Sample_Name'].apply(
+            lambda x: umlautDestroyer(x)
+        )
         # parkour lists requested in millions.
         parkourDF['reqDepth'] = parkourDF['reqDepth']*1000000
         # Some exceptions where there is a ' in the description..

diff --git a/src/dissectBCL/misc.py b/src/dissectBCL/misc.py
@@ -67,9 +67,6 @@ def getConf(configfile, quickload=False):
             print("{} = {}".format(
                 soft, ver
             ))
-            logging.info("{} = {}".format(
-                soft, ver
-                ))
         # Double check if fastqc_adapters is set.
         if not os.path.exists(
             config['software']['fastqc_adapters']