diff --git a/workflow/conf/aws_ondemand.config b/workflow/conf/aws_ondemand.config
index 1a14ebf3dc44d33198c8472a231796f980e312da..84fcb275e131e30ea4a21ad829d67c368dca1811 100755
--- a/workflow/conf/aws_ondemand.config
+++ b/workflow/conf/aws_ondemand.config
@@ -13,14 +13,7 @@ process {
   cpus = 1
   memory = '1 GB'
 
-  withName:getBag {
-    container = 'bicf/gudmaprbkfilexfer:1.3'
-  }
-  withName:getData {
-    container = 'bicf/gudmaprbkfilexfer:1.3'
-  }
   withName:trimData {
-    container = 'bicf/trimgalore:1.1'
     cpus = 15
   }
 }
\ No newline at end of file
diff --git a/workflow/conf/aws_spot.config b/workflow/conf/aws_spot.config
index b5239a2388616beb2936e41020e5c387f87118a6..fbccb3cba394d2a1a7751bee7206483c869eac23 100755
--- a/workflow/conf/aws_spot.config
+++ b/workflow/conf/aws_spot.config
@@ -13,14 +13,7 @@ process {
   cpus = 1
   memory = '1 GB'
 
-  withName:getBag {
-    container = 'bicf/gudmaprbkfilexfer:1.3'
-  }
-  withName:getData {
-    container = 'bicf/gudmaprbkfilexfer:1.3'
-  }
   withName:trimData {
-    container = 'bicf/trimgalore:1.1'
     cpus = 15
   }
 }
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 20da91a7f7a241e610708d7186d299d397958c41..36d5b332611f5d234a692b545819ad44db8c381e 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -5,16 +5,16 @@ process {
 
   withName:getBag {
     executor = 'local'
-    container = 'docker://bicf/gudmaprbkfilexfer:1.3'
   }
   withName:getData {
     executor = 'local'
-    container = 'docker://bicf/gudmaprbkfilexfer:1.3'
   }
   withName:trimData {
-    container = 'docker://bicf/trimgalore:1.1'
     queue = '256GB,256GBv1,384GB'
   }
+  withName:parseMetadata {
+    executor = 'local'
+  }
 }
 
 singularity {
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index 37584999cf8152c9776b676d0b013f8aeb5e8709..2635a79cc3b24090639ed78af92b633994d4208e 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -10,6 +10,21 @@ profiles {
   }
 }
 
+process {
+  withName:getBag {
+    container = 'bicf/gudmaprbkfilexfer:1.3'
+  }
+  withName:getData {
+    container = 'bicf/gudmaprbkfilexfer:1.3'
+  }
+  withName:trimData {
+    container = 'bicf/trimgalore:1.1'
+  }
+  withName:parseMetadata {
+    container = 'bicf/python:1.3'
+  }
+}
+
 trace {
   enabled = true
   file = 'pipeline_trace.txt'
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 6e4199d5edc0b3bc66676d00a99bff44e95051e9..a10a29aed64d68150b1ab1020cfc2c826e7f7346 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -111,6 +111,7 @@ process parseMetadata {
     """
     hostname >>${repRID_parseMetadata}.parseMetadata.err
     ulimit -a >>${repRID_parseMetadata}.parseMetadata.err
+    python ${baseDir}/scripts/parseMeta.py -r ${repRID_parseMetadata} -m ${fileMeta} -p repRID
     """
 
 }
diff --git a/workflow/scripts/parseMeta.py b/workflow/scripts/parseMeta.py
index 115dd6d8da25ade429fac3a8bed3c2f3fa0f78aa..bd872fca3eb1c58101f288527a45c87920b66dcf 100644
--- a/workflow/scripts/parseMeta.py
+++ b/workflow/scripts/parseMeta.py
@@ -14,14 +14,19 @@ def get_args():
 
 def main():
     args = get_args()
-    metaFile = pd.read_csv(args.metaFile,sep="\t",header=None)
+    metaFile = pd.read_csv(args.metaFile,sep=",",header=0)
     if (args.parameter == "repRID"):
         if (len(metaFile.Replicate_RID.unique()) > 1):
-            #ERROR
-        if not (metaFile.Replicate_RID == arg$repRID):
-            #ERROR
-        if (len(fileFile[fileFile["File_Type"] == "FastQ"].RID) > 2):
-            #ERROR
+            print("There are multiple replicate RID's in the metadata: " + " ".join(metaFile.Replicate_RID.unique()))
+            exit(1)
+        if not (metaFile.Replicate_RID.unique() == args.repRID):
+            print("Replicate RID in metadata does not match run parameters: " + metaFile.Replicate_RID.unique() + " vs " + args.repRID)
+            exit(1)
+        else:
+            print(metaFile["Replicate_RID"].unique())
+        if (len(metaFile[metaFile["File_Type"] == "FastQ"]) > 2):
+            print("There are more then 2 fastq's in the metadata: " + " ".join(metaFile[metaFile["File_Type"] == "FastQ"].RID))
+            exit(1)
 
 
 if __name__ == '__main__':