diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index b2723926ff7aab5a97c0cc8a96f03c2f90006282..d839044791bc3aaccc701c9fb62099105c97205b 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -25,14 +25,25 @@ outDir = params.outDir
         file bdbag
 
     output:
-        file("*") into dataPaths
+        file("**/*.R*.fastq.gz") into fastqPaths
+        file("**/File.csv") into filePaths
+        file("**/Experiment Settings.csv") into experimentSettingsPaths
+        file("**/Experiment.csv") into experimentPaths
 
     script:
         """
         hostname
         ulimit -a
+        study=\$(echo "${bdbag}" | cut -d'.' -f1)
+        echo LOG: \${study}
         unzip ${bdbag}
-        python3 ${baseDir}/scripts/modifyFetch.py -f \$(echo "${bdbag}" | cut -d'.' -f1)
-        bdbag --materialize "\$(echo "${bdbag}" | cut -d'.' -f1)"
+        echo LOG: bdgag unzipped
+        python3 ${baseDir}/scripts/modifyFetch.py --fetchFile \${study}
+        echo LOG: fetch file filtered for only .fastq.gz
+        #bdbag --materialize "\$(echo "${bdbag}" | cut -d'.' -f1)"
+        sh ${baseDir}/scripts/bdbagFetch.sh \${study}
+        echo LOG: bdbag fetched
+        sh ${baseDir}/scripts/renameFastq.sh \${study}
+        echo LOG: fastq.gz files renamed to replicate RID
         """
  }
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diff --git a/workflow/scripts/bdbagFetch.sh b/workflow/scripts/bdbagFetch.sh
new file mode 100644
index 0000000000000000000000000000000000000000..28dab3f5338b3b6371b2b8f4ee7ac6bf2e715fa6
--- /dev/null
+++ b/workflow/scripts/bdbagFetch.sh
@@ -0,0 +1,3 @@
+#!/bin
+
+bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz $1
\ No newline at end of file
diff --git a/workflow/scripts/modifyFetch.sh b/workflow/scripts/modifyFetch.sh
deleted file mode 100644
index f243f5cc2ad6e72327e57e249260d662a0876238..0000000000000000000000000000000000000000
--- a/workflow/scripts/modifyFetch.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin
-
-unzip $1
\ No newline at end of file
diff --git a/workflow/scripts/renameFastq.sh b/workflow/scripts/renameFastq.sh
new file mode 100644
index 0000000000000000000000000000000000000000..f5593766b3a3bd645c3f2c8758d3a20fd354c9be
--- /dev/null
+++ b/workflow/scripts/renameFastq.sh
@@ -0,0 +1,15 @@
+#!/bin
+
+while read loc checksum fileLocation
+do
+    file=$(echo ${fileLocation##*/})
+    fileName=$(echo ${file%.R*.fastq.gz})
+    fileExt=$(echo ${file##${fileName}.})
+    while IFS="," read RID Study_RID Experiment_RID Replicate_RID Caption File_Type File_Name URI File_size MD5 GEO_Archival_URL dbGaP_Accession_ID Processed Notes Principal_Investigator Consortium Release_Date RCT RMT Legacy_File_RID GUDMAP_NGF_OID GUDMAP_NGS_OID
+    do
+        if [ ${file} == ${File_Name} ]
+        then
+            find . -type f -name ${file} -execdir mv {} ${Replicate_RID}.${fileExt} ';'
+        fi
+    done < $1/data/File.csv
+done < $1/fetch.txt
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