solved extra pars in 10x demux for masking

epigen-UCSD · Dec 12, 2019 · 46dd50b · 46dd50b
1 parent b6308cb
commit 46dd50b
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Showing 2 changed files with 11 additions and 3 deletions.
diff --git a/nextseq_app/models.py b/nextseq_app/models.py
@@ -39,7 +39,7 @@ class RunInfo(models.Model):
         max_length=2, choices=read_type_choice, default='PE', help_text='default:PE')
     experiment_type = models.CharField(max_length=2, choices=exp_type_choice,
                                        default='BK', help_text='bulk (default), snATAC_v2:combinatory barcode v2, 10xATAC, 10xRNAseq, bulk_10xATAC')
-    total_reads = models.IntegerField(blank=True, null=True)
+    total_reads = models.BigIntegerField(blank=True, null=True)
     total_libraries = models.IntegerField(blank=True, null=True)
     percent_of_reads_demultiplexed = models.IntegerField(blank=True, null=True)
     read_length = models.CharField(

diff --git a/nextseq_app/views.py b/nextseq_app/views.py
@@ -755,8 +755,12 @@ def DemultiplexingView(request, run_pk):
             cmd1 = './utility/runDemuxSnATAC.sh ' + runinfo.Flowcell_ID + \
                 ' ' + basedirname + ' ' + request.user.email
         elif runinfo.experiment_type == 'TA':
+            # write extra_parameters to disk
+            with open( os.path.join(basedirname, 'Data/Fastqs/', 'extraPars.txt'),'w') as out:
+                out.write(runinfo.extra_parameters)
+
             cmd1 = './utility/runDemux10xATAC.sh ' + runinfo.Flowcell_ID + \
-                ' ' + basedirname + ' ' + request.user.email + ' ' +runinfo.extra_parameters
+                ' ' + basedirname + ' ' + request.user.email
         else:
             cmd1 = './utility/runBcl2fastq.sh ' + runinfo.Flowcell_ID + \
                 ' ' + basedirname + ' ' + request.user.email
@@ -906,8 +910,12 @@ def DemultiplexingView2(request, run_pk):
             cmd1 = './utility/runDemuxSnATAC.sh ' + runinfo.Flowcell_ID + \
                 ' ' + basedirname + ' ' + request.user.email
         elif runinfo.experiment_type == 'TA':
+            # write extra_parameters to disk
+            with open( os.path.join(basedirname, 'Data/Fastqs/', 'extraPars.txt'),'w') as out:
+                out.write(runinfo.extra_parameters)
+
             cmd1 = './utility/runDemux10xATAC.sh ' + runinfo.Flowcell_ID + \
-                ' ' + basedirname + ' ' + request.user.email + ' '  + runinfo.extra_parameters 
+                ' ' + basedirname + ' ' + request.user.email
         else:
             cmd1 = './utility/runBcl2fastq.sh ' + runinfo.Flowcell_ID + \
                 ' ' + basedirname + ' ' + request.user.email