diff --git a/workflow/conf/replicate_export_config.json b/workflow/conf/replicate_export_config.json
index ff17fa513c5bc130a2e2bdaf9aa41b070c99b290..4380e46734a4425f7df57ad0cf0553a868b03c9d 100644
--- a/workflow/conf/replicate_export_config.json
+++ b/workflow/conf/replicate_export_config.json
@@ -1,6 +1,6 @@
 {
   "bag": {
-    "bag_name": "Replicate_{rid}",
+    "bag_name": "{rid}_inputBag",
     "bag_algorithms": [
       "md5"
     ],
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 09d35d6c7943d78924dbc0aeac3dc4bcae58d681..ccedc85a24ee1856d4284d6b2f92595cde55b125 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -157,7 +157,7 @@ process getBag {
     path replicateExportConfig
 
   output:
-    path ("Replicate_*.zip") into bag
+    path ("*.zip") into bag
 
   when:
     inputBagForce == ""
@@ -222,7 +222,7 @@ process getData {
     echo -e "LOG: linked" >> ${repRID}.getData.log
 
     # get bag basename
-    replicate=\$(basename "${inputBag}" | cut -d "." -f1)
+    replicate=\$(basename "${inputBag}" | cut -d "_" -f1)
     echo -e "LOG: bag replicate name \${replicate}" >> ${repRID}.getData.log
 
     # unzip bag
@@ -1511,10 +1511,11 @@ process outputBag {
   hostname > ${repRID}.outputBag.log
   ulimit -a >> ${repRID}.outputBag.log
 
-  mkdir -p ./deriva/Seq/Workflow_Runs/${studyRID}/${executionRunRID}/
-  cp ${bam} ./deriva/Seq/Workflow_Runs/${studyRID}/${executionRunRID}/
-  cp ${bigwig} ./deriva/Seq/Workflow_Runs/${studyRID}/${executionRunRID}/
-  cp ${counts} ./deriva/Seq/Workflow_Runs/${studyRID}/${executionRunRID}/
+  mkdir -p ./deriva/Seq/pipeline/${studyRID}/${executionRunRID}/
+  cp ${bam} ./deriva/Seq/pipeline/${studyRID}/${executionRunRID}/
+  cp ${bai} ./deriva/Seq/pipeline/${studyRID}/${executionRunRID}/
+  cp ${bigwig} ./deriva/Seq/pipeline/${studyRID}/${executionRunRID}/
+  cp ${counts} ./deriva/Seq/pipeline/${studyRID}/${executionRunRID}/
 
   cookie=\$(cat credential.json | grep -A 1 '\\"${source}\\": {' | grep -o '\\"cookie\\": \\".*\\"')
   cookie=\${cookie:20:-1}
diff --git a/workflow/scripts/bdbagFetch.sh b/workflow/scripts/bdbagFetch.sh
index 606b88397d5a6cf4feb4aa38d7615e3e3ba48735..1cab13098ce042e03a8a7506b551323f2c24c2e5 100644
--- a/workflow/scripts/bdbagFetch.sh
+++ b/workflow/scripts/bdbagFetch.sh
@@ -2,7 +2,7 @@
 
 if [ -z "${3}" ]
 then
-    bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1}
+    bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1}_inputBag
     for i in $(find */ -name "*R*.fastq.gz")
     do
         path=${2}.$(echo ${i##*/} | grep -o "R[1,2].fastq.gz")