Main (#186)

env.yml

@@ -18,7 +18,7 @@ dependencies:
   - rich-click >=1.5
   - biopython >=1.7
   - bbmap >= 38.98
-  - multiqc >= 1.12
+  - multiqc >= 1.21
   - fastqc >= 0.11.9
   - kraken2 >= 2.1.2
   - blast >= 2.13.0

src/dissectBCL/fakeNews.py

@@ -527,23 +527,29 @@ def shipFiles(outPath, config):
         'Illumina_{}'.format(yrstr),
         outLane
     )
+    logging.info(f"Using {seqFacDir} to populate samba dir.")
     if not os.path.exists(seqFacDir):
         pathlib.Path(
             seqFacDir
         ).mkdir(parents=True, exist_ok=True)
-    for qcRepo in glob.glob(
-        os.path.join(outPath, 'Project_*', 'multiqc_report.html')
-    ):
+    _mqcreports = glob.glob(
+        os.path.join(outPath, '*', '*multiqc_report.html')
+    )
+    if not _mqcreports:
+        logging.warning(f"No multiqcreports found under {outLane}")
+    for qcRepo in _mqcreports:
         # to seqfacdir
         outqcRepo = os.path.join(
             seqFacDir, qcRepo.split('/')[-2] + '_multiqcreport.html'
         )
+        logging.info(f"Copying {qcRepo} over to {outqcRepo}")
         shutil.copyfile(qcRepo, outqcRepo)
         # to bioinfoCoredir
         outqcBioinfo = os.path.join(
             config['Dirs']['bioinfoCoreDir'],
             qcRepo.split('/')[-2] + '_multiqcreport.html'
         )
+        logging.info(f"Copying {qcRepo} over to {outqcBioinfo}")
         shutil.copyfile(qcRepo, outqcBioinfo)
     transferStop = datetime.datetime.now()
     transferTime = transferStop - transferStart

src/dissectBCL/misc.py

@@ -9,7 +9,6 @@
 from importlib.metadata import version
 import sys
 import logging
-import shutil
 
 
 def getConf(configfile, quickload=False):
@@ -338,6 +337,9 @@ def formatMisMatches(mmDic):
     return (retStr[:-2])
 
 
+'''
+Uncomment the shutil
+
 def fetchLatestSeqDir(PIpath, seqDir):
     # fetch sorted sequence_data directories ascending
     seqDirs = sorted(
@@ -357,6 +359,24 @@ def fetchLatestSeqDir(PIpath, seqDir):
         "No seq_data dir for {} found with space. Exiting.".format(PIpath)
     )
     sys.exit()
+'''
+
+
+def fetchLatestSeqDir(PIpath, seqDir):
+    '''
+    Fetch the latest sequencing_data dir in the PI directory
+    '''
+    seqDirNum = 0
+    for dirs in os.listdir(os.path.join(PIpath)):
+        if seqDir in dirs:
+            seqDirStrip = dirs.replace('sequencing_data', '')
+            if seqDirStrip != '':
+                if int(seqDirStrip) > seqDirNum:
+                    seqDirNum = int(seqDirStrip)
+    if seqDirNum == 0:
+        return os.path.join(PIpath + '/sequencing_data')
+    else:
+        return os.path.join(PIpath + '/sequencing_data' + str(seqDirNum))
 
 
 def umlautDestroyer(germanWord):