Ruamel api (#179)

dissectBCL.ini

@@ -28,6 +28,7 @@ mpiImg=/path/to/multiqc_headerimg.jpg
 krakenExpl="<font size="2"> Kraken is used to classify the reads and to detect contamination. <br> For this we use a *custom* database, with a simplified taxonomical hierarchy (that no longer resembles any true taxonomical classification. <br> In brief, by default we screen for: <li><b>eukaryotes</b> (human, mouse, fly, mosquito, lamprey, medaka, c-elegans, yeast, zebrafish and the moss-piglet)</li> <li><b>prokaryotes</b> (Ecoli, pseudomonas, mycoplasma and haemophilus influenza)</li> <li><b>viruses</b> (sars-cov2, influenza A,B & C, norwalk virus, rhinoviruses, drosophila C virus, phiX and lambda phage )</li> <li><b>custom databases</b> (ERCC spikes, univec core DB)</li> Note that for human, mouse, fly and mosquito we scan for mitochondrial and ribosomal contamination separately). <br> Only the top (most abundant) five hits and unclassified hits are shown, all other hits are grouped under an 'other' tag.</font>"   
 
 [communication]
+subject=dissectBCL
 deepSeq[email protected]
 bioinfoCore[email protected]
 fromAddress[email protected]

src/dissectBCL/fakeNews.py

@@ -360,7 +360,8 @@ def multiQC_yaml(config, flowcell, ssDic, project, laneFolder):
 
 def mailHome(subject, _html, config, toCore=False):
     mailer = MIMEMultipart('alternative')
-    mailer['Subject'] = '[dissectBCL] [{}] '.format(
+    mailer['Subject'] = '[{}] [{}] '.format(
+        config['communication']['subject'],
         version('dissectBCL')
     ) + subject
     mailer['From'] = config['communication']['fromAddress']
@@ -580,21 +581,30 @@ def organiseLogs(flowcell, sampleSheet):
                     mvFile
                 )
                 shutil.move(fileIn, fileOut)
+
         # Write out ssdf.
         outssdf = os.path.join(_logDir, 'sampleSheetdf.tsv')
         sampleSheet.ssDic[outLane]['sampleSheet'].to_csv(outssdf, sep='\t')
-        # Write out the yaml files.
-        yaml = ruamel.yaml.YAML()
-        yaml.indent(mapping=2, sequence=4, offset=2)
 
         # write out outLaneInfo.yaml
+        dic0 = sampleSheet.ssDic[outLane]
+        del dic0['sampleSheet']
+        yaml0 = ruamel.yaml.YAML()
+        yaml0.indent(mapping=2, sequence=4, offset=2)
         outLaneInfo = os.path.join(_logDir, 'outLaneInfo.yaml')
-        dic = sampleSheet.ssDic[outLane]
-        del dic['sampleSheet']
         with open(outLaneInfo, 'w') as f:
-            ruamel.yaml.dump(dic, f)
+            yaml0.dump(dic0, f)
+
+        # write out config.ini
+        dic1 = flowcell.asdict()
+        flowcellConfig = os.path.join(_logDir, 'config.ini')
+        with open(flowcellConfig, 'w') as f:
+            dic1['config'].write(f)
+
         # write out flowcellInfo.yaml
+        del dic1['config']
+        yaml1 = ruamel.yaml.YAML()
+        yaml1.indent(mapping=2, sequence=4, offset=2)
         flowcellInfo = os.path.join(_logDir, 'flowcellInfo.yaml')
-        dic = flowcell.asdict()
         with open(flowcellInfo, 'w') as f:
-            ruamel.yaml.dump(dic, f)
+            yaml1.dump(dic1, f)

src/dissectBCL/misc.py

@@ -156,7 +156,7 @@ def hamming(s1, s2):
     # We have some basket cases (multimodal)
     # Where barcode is nan (type as float)
     # Ignore these for now.
-    if type(s1) == float or type(s2) == float:
+    if isinstance(s1, float) or isinstance(s2, float):
         return 0
     if s1 is None or s2 is None:
         return 0

src/tools/emailProjectFinished.py

@@ -134,11 +134,9 @@ def main():
         if not os.path.exists(p):
             sys.exit("Project folder {} not found.".format(p))
 
-    # get lastName (user) from project name
-    lastName = args.project[0].split("_")[2]
+    # get user from project name, lastName = args.project[0].split("_")[2]
     if not args.toEmail or not args.toName:
         my_dict = getContactDetails(args.project[0].split("_")[1], config)
-        assert lastName == my_dict["last_name"]
         firstName, email = my_dict["first_name"], my_dict["email"]
     else:
         firstName, email = args.toName, args.toEmail