Merge pull request #48 from snsansom/unpaired

minor fixes

Author: snsansom

pipelines/pipeline_scrnaseq.py

@@ -1258,7 +1258,7 @@ def numberGenesDetectedFeatureCounts(infile, outfile):
                    on h.gene_id=i.gene_id
                ''' % locals()
 
-    melted_df = DB.fetch_DataFrame(statement, DATABASE, attach)
+    melted_df = DB.fetch_DataFrame(statement, DATABASE, str(attach))
 
     grouped_df = melted_df.groupby(["gene_biotype", "track"])
 

pipelines/pipeline_scrnaseq/pipeline.ini

@@ -182,7 +182,7 @@ geneset_flat=/gfs/mirror/ucsc/mm10/database/refFlat.txt.gz
 validation_stringency=SILENT
 threads=3
 # Set the total memory required by all threads *in megabytes*.
-total_mb_memory=4000
+total_mb_memory=8000
 
 # use to pass additional options to picard
 alignmentsummarymetrics_options=