From 0f995fe32e19dbff1917d3b529ff3c74f410c062 Mon Sep 17 00:00:00 2001
From: WardDeb <ward@deboutte.be>
Date: Tue, 25 Apr 2023 17:01:13 +0200
Subject: [PATCH] update email with some red

---
 src/dissectBCL/classes.py | 10 ++++++++--
 src/dissectBCL/demux.py   |  3 +++
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/src/dissectBCL/classes.py b/src/dissectBCL/classes.py
index 2f33c18..7900ae9 100644
--- a/src/dissectBCL/classes.py
+++ b/src/dissectBCL/classes.py
@@ -402,8 +402,6 @@ def spaceGood(freeSpace):
                     message += "return {}: {}\n".format(
                         subkey, self.exitStats[key][subkey]
                     )
-        if self.P5RC:
-            message += "\nNote that the P5s have been reverse complemented automatically!\n"
 
         # undetermined table
         undtableHead = ["P7", "P5", "# reads (M)", "% of und. Reads"]
@@ -481,7 +479,14 @@ def optDupRet(optDup):
                     parkourOrg  # parkourOrg
                 ]
             )
+        if not self.P5RC:
+            P5RCstr = ''
+        else:
+            P5RCstr = '\n\nNote that the <FONT COLOR=red><strong>P5s have been reverse complemented automatically</strong></FONT> !'
+            P5RCstr += '\nThe multiQC report contains the barcodes as they are used for demultiplexing.\n'
+        
         msg = _html.render() +\
+            P5RCstr +\
             '<h3>Top unknown barcodes</h3>' +\
             tabulate(undtableCont, undtableHead, tablefmt="html") +\
             '<h3>Samples</h3>' +\
@@ -522,3 +527,4 @@ def __init__(
         self.mismatch = mismatch
         self.transferTime = transferTime
         self.exitStats = exitStats
+        self.P5RC = P5RC
diff --git a/src/dissectBCL/demux.py b/src/dissectBCL/demux.py
index 9ba1ec1..0de26bc 100644
--- a/src/dissectBCL/demux.py
+++ b/src/dissectBCL/demux.py
@@ -505,6 +505,9 @@ def demux(sampleSheet, flowcell, config):
                 sampleSheet.ssDic[outLane]['sampleSheet'],
                 manual_df
             )
+            # Check for 'bak file' existence.
+            if os.path.exists(demuxOut + '.bak'):
+                sampleSheet.ssDic[outLane]['P5RC'] = True
         # Don't run bcl-convert if we have the touched flag.
         if not os.path.exists(
             os.path.join(outputFolder, 'bclconvert.done')