diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 10b06f97a6a83b23bdb1ac01e2ce46e975def353..6e1028aba7a0d2969e4766b210f1c13c30d0c538 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -51,11 +51,11 @@ trimData:
 alignData:
   stage: unit
   script:
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.se.unal.gz -S Q-Y5JA_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/Q-Y5JA_1M_trimmed.fq.gz
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.se.unal.gz -S Q-Y5JA_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/Q-Y5JA_1M_trimmed.fq.gz
   - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o Q-Y5JA_1M.se.bam Q-Y5JA_1M.se.sam
   - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.bam
   - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.sorted.bai
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.pe.unal.gz -S Q-Y5JA_1M.pe.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/small/Q-Y5JA_1M_R1_val_1.fq.gz -2 ./test_data/fastq/small/Q-Y5JA_1M_R2_val_2.fq.gz
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.pe.unal.gz -S Q-Y5JA_1M.pe.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/small/Q-Y5JA_1M_R1_val_1.fq.gz -2 ./test_data/fastq/small/Q-Y5JA_1M_R2_val_2.fq.gz
   - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o Q-Y5JA_1M.pe.bam Q-Y5JA_1M.pe.sam
   - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA_1M.pe.sorted.bam Q-Y5JA_1M.pe.bam
   - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA_1M.pe.sorted.bam Q-Y5JA_1M.pe.sorted.bai
@@ -64,8 +64,16 @@ alignData:
 dedupData:
   stage: unit
   script:
-  - singularity exec 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5JA_1M.se.sorted.bam O=Q-Y5JA_1M.se.deduped.bam M=Q-Y5JA_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
+  - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5JA_1M.se.sorted.bam O=Q-Y5JA_1M.se.deduped.bam M=Q-Y5JA_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
+  - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA_1M.se.sorted.deduped.bam ./test_data/bam/small/Q-Y5JA_1M.se.deduped.bam
+  - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools index -@ `nproc` -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam Q-Y5JA_1M.se.sorted.deduped.bai
   - pytest -m dedupData
+  
+makeBigWig:
+  stage: unit
+  script:
+  - singularity run 'docker://bicf/deeptools3.3:2.0.0' bamCoverage -p `nproc` -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam -o Q-Y5JA_1M.se.bw
+  - pytest -m makeBigWig
 
 fastqc:
   stage: unit
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 56e7e6aa9abb7b1ce87fbc6cf9857c0460f140d5..a6f5fba4f7f6600733c0accce8d853fefb1fce63 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -27,6 +27,9 @@ process {
   withName: fastqc {
     queue = 'super'
   }
+  withName: makeBigWig {
+    queue = 'super'
+  }
 }
 
 singularity {
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index 02c71af5c58998839c270f78aadfdfd84696dfa3..eee32fa6f754c55b6b8051eedee646eebf4066c2 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -30,11 +30,14 @@ process {
     container = 'bicf/gudmaprbkaligner:2.0.0'
   }
   withName: dedupData {
-    container = 'bicf/picard2.21.7:2.0.0'
+    container = 'bicf/gudmaprbkdedup:2.0.0'
   }
   withName: fastqc {
     container = 'bicf/fastqc:2.0.0'
   }
+  withName: makeBigWig {
+    container = 'bicf/deeptools3.3:2.0.0'
+  }
 }
 
 trace {
@@ -64,4 +67,4 @@ manifest {
   mainScript = 'rna-seq.nf'
   version = 'v0.0.1_indev'
   nextflowVersion = '>=19.09.0'
-}
\ No newline at end of file
+}
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 0fd3ee0d872768d1d7d80c0be6bcc0cbafd105e0..28770ca170ed49a1524122852898337286c6aecb 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1,13 +1,20 @@
 #!/usr/bin/env nextflow
 
+//  ########  ####  ######  ######## 
+//  ##     ##  ##  ##    ## ##       
+//  ##     ##  ##  ##       ##       
+//  ########   ##  ##       ######   
+//  ##     ##  ##  ##       ##       
+//  ##     ##  ##  ##    ## ##       
+//  ########  ####  ######  ##       
+
 // Define input variables
 params.deriva = "${baseDir}/../test_data/auth/credential.json"
 params.bdbag = "${baseDir}/../test_data/auth/cookies.txt"
 //params.repRID = "16-1ZX4"
 params.repRID = "Q-Y5JA"
-params.refVersion = "0.0.1"
-params.refMuVersion = "38.P6"
-params.refHuVersion = "38.p12"
+params.refMoVersion = "38.p6.vM22"
+params.refHuVersion = "38.p12.v31"
 params.outDir = "${baseDir}/../output"
 
 // Parse input variables
@@ -18,15 +25,15 @@ bdbag = Channel
   .fromPath(params.bdbag)
   .ifEmpty { exit 1, "deriva cookie file for bdbag not found: ${params.bdbag}" }
 repRID = params.repRID
-refVersion = params.refVersion
-refMuVersion = params.refMuVersion
+refMoVersion = params.refMoVersion
 refHuVersion = params.refHuVersion
 outDir = params.outDir
 logsDir = "${outDir}/Logs"
 
 // Define fixed files
 derivaConfig = Channel.fromPath("${baseDir}/conf/replicate_export_config.json")
-referenceBase = "s3://bicf-references"
+//referenceBase = "s3://bicf-references"
+referenceBase = "/project/BICF/BICF_Core/shared/gudmap/references"
 
 // Define script files
 script_bdbagFetch = Channel.fromPath("${baseDir}/scripts/bdbagFetch.sh")
@@ -186,9 +193,11 @@ stranded.into {
 }
 spike.into{
   spike_getRef
+  spike_rseqc
 }
 species.into {
   species_getRef
+  species_rseqc
 }
 
 /*
@@ -199,10 +208,6 @@ process getRef {
   publishDir "${logsDir}", mode: "copy", pattern: "*.getRef.err"
 
   input:
-    val referenceBase
-    val refVersion
-    val refMuVersion
-    val refHuVersion
     val spike_getRef
     val species_getRef
 
@@ -215,13 +220,13 @@ process getRef {
     ulimit -a >>${repRID}.getRef.err
     export https_proxy=\${http_proxy}
 
-    # retreive appropriate reference from S3 bucket
+    # run set the reference name
     if [ "${species_getRef}" == "Mus musculus" ]
     then
-      references=\$(echo ${referenceBase}/mouse/${refVersion}/GRCm${refMuVersion})
+      references=\$(echo ${referenceBase}/GRCm${refMoVersion})
     elif [ '${species_getRef}' == "Homo sapiens" ]
     then
-      references=\$(echo ${referenceBase}/human/${refVersion}/GRCh${refHuVersion})
+      references=\$(echo ${referenceBase}/GRCh${refHuVersion})
     else
       exit 1
     fi
@@ -232,7 +237,17 @@ process getRef {
     then
       reference=\$(echo \${references}/)
     fi
-    aws s3 cp "\${references}" ./ --recursive >>${repRID}.getRef.err
+
+    # retreive appropriate reference appropriate location
+    if [ ${referenceBase} == "s3://bicf-references" ]
+    then
+      aws s3 cp "\${references}" /hisat2 ./ --recursive >>${repRID}.getRef.err
+      aws s3 cp "\${references}" /bed ./ --recursive >>${repRID}.getRef.err
+    elif [ ${referenceBase} == "/project/BICF/BICF_Core/shared/gudmap/references" ]
+    then
+      cp -R "\${references}"/hisat2 ./ >>${repRID}.getRef.err
+      cp -R "\${references}"/bed ./ >>${repRID}.getRef.err
+    fi
     """
 }
 
@@ -268,6 +283,11 @@ process trimData {
     """
 }
 
+reference.into {
+  reference_alignData
+  reference_rseqc
+}
+
 /*
  * alignData: aligns the reads to a reference database
 */
@@ -279,7 +299,7 @@ process alignData {
     val endsManual_alignData
     val stranded_alignData
     path fastq from fastqs_trimmed
-    path reference
+    path reference_alignData
 
   output:
     path ("${repRID}.sorted.bam") into rawBam
@@ -320,7 +340,7 @@ process dedupData {
     path rawBam
 
   output:
-    path ("${repRID}.deduped.bam") into dedupBam
+    tuple val ("${repRID}"), path ("${repRID}.sorted.deduped.bam"), path ("${repRID}.sorted.deduped.bai") into dedupBam
     path ("${repRID}.dedup.out")
     path ("${repRID}.dedup.err")
 
@@ -331,6 +351,8 @@ process dedupData {
 
     # remove duplicated reads
     java -jar /picard/build/libs/picard.jar MarkDuplicates I=${rawBam} O=${repRID}.deduped.bam M=${repRID}.deduped.Metrics.txt REMOVE_DUPLICATES=true 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
+    samtools sort -@ `nproc` -O BAM -o ${repRID}.sorted.deduped.bam ${repRID}.deduped.bam 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
+    samtools index -@ `nproc` -b ${repRID}.sorted.deduped.bam ${repRID}.sorted.deduped.bai 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
     """
 }
 
@@ -356,4 +378,23 @@ process fastqc {
     # run fastqc
     fastqc *.fastq.gz -o . >>${repRID}.fastqc.err
     """
-}
\ No newline at end of file
+}
+
+/*
+ *Make BigWig files for later processes
+*/
+process makeBigWig {
+  tag "${repRID}"
+  publishDir "${logsDir}", mode: 'copy', pattern: "*.makeBigWig.err"
+
+  input:
+    set val (repRID), path (inBam), path (inBai) from dedupBam
+
+  output:
+    path ("${repRID}.bw")
+
+  script:
+    """
+    bamCoverage -p `nproc` -b ${inBam} -o ${repRID}.bw
+    """
+}
diff --git a/workflow/tests/test_makeBigWig.py b/workflow/tests/test_makeBigWig.py
new file mode 100644
index 0000000000000000000000000000000000000000..198b5d2d4cdecd9013e08fbe3eae9c9b7303ef1a
--- /dev/null
+++ b/workflow/tests/test_makeBigWig.py
@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+
+import pytest
+import pandas as pd
+import os
+import utils
+
+data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+	'/../../'
+
+
+@pytest.mark.makeBigWig
+def test_makeBigWig():
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.bw'))