diff --git a/workflow/conf/aws.config b/workflow/conf/aws.config
index 9ecbfb98f593f167a35650299921adaf2fffbb42..b5054f724c810b4eeaa01ae03e6db1ae421ab0cc 100644
--- a/workflow/conf/aws.config
+++ b/workflow/conf/aws.config
@@ -80,4 +80,8 @@ process {
     cpus = 2
     memory = '1 GB'
   }
+  withName: outputBag {
+    cpus = 1
+    memory = '1 GB'
+  }
 }
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 338cd5d54d4258e499a60241054c5f28109e7c19..1bcf1d4e9a51d6ec4f6ffbc594dc09624d019f2e 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -54,6 +54,9 @@ process {
   withName: aggrQC {
     executor = 'local'
   }
+  withName: outputBag {
+    executor = 'local'
+  }
 }
 
 singularity {
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index db422b68cb4a8d1900cbae33801f6d5f5b8eb9a0..0beef33519cf7b9a19d24180256cf6547519403c 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -67,6 +67,9 @@ process {
   withName: aggrQC {
     container = 'bicf/multiqc1.8:2.0.1_indev'
   }
+  withName:outputBag {
+    container = 'bicf/gudmaprbkfilexfer:2.0.1_indev'
+  }
 }
 
 trace {
@@ -94,6 +97,6 @@ manifest {
   homePage = 'https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq'
   description = 'This pipeline was created to be a standard mRNA-sequencing analysis pipeline which integrates with the GUDMAP and RBK consortium data-hub.'
   mainScript = 'rna-seq.nf'
-  version = 'v0.0.1'
+  version = 'v0.0.2_indev'
   nextflowVersion = '>=19.09.0'
 }
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 5b03e5a2efa11cc13e2e342c646ce0d03add9068..7d5e1d397a9dd74ce0b5a90605dfa90a04af3e2c 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1058,4 +1058,28 @@ process aggrQC {
     multiqc -c ${multiqcConfig} . -n ${repRID}.multiqc.html
     cp ${repRID}.multiqc_data/multiqc_data.json ${repRID}.multiqc_data.json
     """
-}
\ No newline at end of file
+}
+
+/*
+ *ouputBag: create ouputBag
+*/
+process outputBag {
+  tag "${repRID}"
+  publishDir "${outDir}/outputBag", mode: 'copy', pattern: "Replicate_${repRID}.outputBag.zip"
+  
+  input:
+    path multiqc
+    path multiqcJSON
+  
+  output:
+    path ("Replicate_*.zip") into outputBag
+
+  script:
+  """
+  mkdir Replicate_${repRID}.outputBag
+  cp ${multiqc} Replicate_${repRID}.outputBag
+  cp ${multiqcJSON} Replicate_${repRID}.outputBag
+  bdbag Replicate_${repRID}.outputBag --archiver zip
+  """
+}
+