diff --git a/.gitignore b/.gitignore
index 9b75a201f875574a221bd0e4bf073e5a0d0db406..f86b65e13780bc14b987372cb35d5dd8e310adcc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -298,4 +298,4 @@ timeline*.html*
 *.out
 run*.sh
 
-!.gitkeep
+!.gitkeep
\ No newline at end of file
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index edff72458a74626000a40e0802fe01872fbe5aad..37083c154c27c879833b85c8f8c256c2aecb46dc 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -32,33 +32,38 @@ parseMetadata:
   - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p repRID
   - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p ends
   - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsManual
-  - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded
-  - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p specie
+  - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded -e se
+  - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species
+
+getRef:
+  stage: unit
+  script:
+  - singularity run 'docker://bicf/awscli:1.1' aws s3 ls s3://bicf-references/mouse/0.0.1/GRCm38.P6
+  - singularity run 'docker://bicf/awscli:1.1' aws s3 ls s3://bicf-references/human/0.0.1/GRCh38.p12
 
 trimData:
   stage: unit
   script:
-  - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --basename 16-1ZX4 -j `nproc` ./test_data/fastq/16-1ZX4.R1.fastq.gz
-  - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --paired --basename Q-Y5JA -j `nproc` ./test_data/fastq/Q-Y5JA.R1.fastq.gz ./test_data/fastq/Q-Y5JA.R2.fastq.gz
+  - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --basename Q-Y5JA_1M.se -j `nproc` ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz
+  - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --paired --basename Q-Y5JA_1M.pe -j `nproc` ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5JA_1M.R2.fastq.gz
   - pytest -m trimData
 
-alignReads:
+alignData:
   stage: unit
   script:
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA.unal.gz -S Q-Y5JA.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/Q-Y5JA_R1_val_1.fq.gz -2 ./test_data/fastq/Q-Y5JA_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.bam Q-Y5JA.sam
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA.sorted.bam Q-Y5JA.bam
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA.sorted.bam Q-Y5JA.sorted.bai
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz 16-1ZX4.unal.gz -S 16-1ZX4.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness FR -U ./test_data/fastq/16-1ZX4_trimmed.fq.gz
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o 16-1ZX4.bam 16-1ZX4.sam
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o 16-1ZX4.sorted.bam 16-1ZX4.bam
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b 16-1ZX4.sorted.bam 16-1ZX4.sorted.bai
+  - 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' 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' 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
   - pytest -m alignData
 
-dedupReads:
+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.pe.sorted.bam O=Q-Y5JA_1M.pe.deduped.bam M=Q-Y5JA_1M.pe.deduped.Metrics.txt REMOVE_DUPLICATES=true
   - 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
   - pytest -m dedupData
 
@@ -70,4 +75,4 @@ integration_se:
 integration_pe:
   stage: integration
   script:
-  - nextflow run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA
+  - nextflow run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA
\ No newline at end of file
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9345688f2a0ae3ee68fb31d2947a772882c51926..8ff0911406a181f08e86e495c7530f87d6f43dae 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,8 +1,6 @@
 # v0.0.1 (in development)
 **User Facing**
-* Raw alignment files
 
 **Background**
-* Implementation of CI
 
 *Known Bugs*
diff --git a/workflow/conf/aws_ondemand.config b/workflow/conf/aws_ondemand.config
index 84fcb275e131e30ea4a21ad829d67c368dca1811..ca23b6c49cd80b98c3120010609d46e7131757f8 100755
--- a/workflow/conf/aws_ondemand.config
+++ b/workflow/conf/aws_ondemand.config
@@ -13,7 +13,22 @@ process {
   cpus = 1
   memory = '1 GB'
 
+  withName:parseMetadata {
+    cpus = 5
+  }
+  withName:getRef {
+    cpus = 8
+  }
   withName:trimData {
-    cpus = 15
+    cpus = 8
+    memory = '2 GB'
+  }
+  withName:alignData {
+    cpus = 50
+    memory = '10 GB'
+  }
+  withName:dedupData {
+    cpus = 2
+    memory = '20 GB'
   }
 }
\ No newline at end of file
diff --git a/workflow/conf/aws_spot.config b/workflow/conf/aws_spot.config
index fbccb3cba394d2a1a7751bee7206483c869eac23..e0447565495e09c3ccde2968eb887aa14f7db251 100755
--- a/workflow/conf/aws_spot.config
+++ b/workflow/conf/aws_spot.config
@@ -13,7 +13,22 @@ process {
   cpus = 1
   memory = '1 GB'
 
+  withName:parseMetadata {
+    cpus = 5
+  }
+  withName:getRef {
+    cpus = 8
+  }
   withName:trimData {
-    cpus = 15
+    cpus = 8
+    memory = '2 GB'
+  }
+  withName:alignData {
+    cpus = 50
+    memory = '10 GB'
+  }
+  withName:dedupData {
+    cpus = 2
+    memory = '20 GB'
   }
 }
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index dbc4e53bdc004d1bc61e52806bc9a94d7f7634cd..a17f91e1a3397c2c28fe84d0e70b2342f32cbb0a 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -12,14 +12,17 @@ process {
   withName:parseMetadata {
     executor = 'local'
   }
+  withName:getRef {
+    executor = 'local'
+  }
   withName:trimData {
-    queue = '256GB,256GBv1,384GB'
+    queue = 'super'
   }
-  withName:alignReads {
-    queue = '256GB,256GBv1,384GB'
+  withName:alignData {
+    queue = '256GB,256GBv1'
   }
-  withName: dedupReads {
-    queue = '128GB,256GB,256GBv1,384GB'
+  withName: dedupData {
+    queue = 'super'
   }
 }
 
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index 67cb95ebd958c861697dad2eede6b906cc728669..0b6f27a5c078db72a5ae025a5d0cde2118163047 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -20,13 +20,16 @@ process {
   withName:parseMetadata {
     container = 'bicf/python3:1.3'
   }
+  withName:getRef {
+    container = 'bicf/awscli:1.1'
+  }
   withName:trimData {
     container = 'bicf/trimgalore:1.1'
   }
-  withName: alignReads {
+  withName: alignData {
     container = 'bicf/gudmaprbkaligner:2.0.0'
   }
-  withName: dedupReads {
+  withName: dedupData {
     container = 'bicf/picard2.21.7:2.0.0'
   }
 }
@@ -58,4 +61,4 @@ 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 a15e439d5eb8ab5bd3a53c941733360c159c0470..740db3bc6973c950339127ba8d81934766ad085f 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -5,8 +5,10 @@ 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.outDir = "${baseDir}/../output"
-params.reference = "/project/BICF/BICF_Core/shared/gudmap/references"
 
 // Parse input variables
 deriva = Channel
@@ -16,12 +18,15 @@ bdbag = Channel
   .fromPath(params.bdbag)
   .ifEmpty { exit 1, "deriva cookie file for bdbag not found: ${params.bdbag}" }
 repRID = params.repRID
+refVersion = params.refVersion
+refMuVersion = params.refMuVersion
+refHuVersion = params.refHuVersion
 outDir = params.outDir
-referenceBase = file ("${params.reference}")
 logsDir = "${outDir}/Logs"
 
 // Define fixed files
 derivaConfig = Channel.fromPath("${baseDir}/conf/replicate_export_config.json")
+referenceBase = "s3://bicf-references"
 
 // Define script files
 script_bdbagFetch = Channel.fromPath("${baseDir}/scripts/bdbagFetch.sh")
@@ -32,15 +37,15 @@ script_parseMeta = Channel.fromPath("${baseDir}/scripts/parseMeta.py")
  */
 process getBag {
   tag "${repRID}"
-  publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.getBag.err"
+  publishDir "${logsDir}", mode: "copy", pattern: "*.getBag.err"
 
   input:
-    path credential, stageAs: 'credential.json' from deriva
+    path credential, stageAs: "credential.json" from deriva
     path derivaConfig
 
   output:
     path ("Replicate_*.zip") into bagit
-    file ("${repRID}.getBag.err")
+    path ("${repRID}.getBag.err")
 
   script:
     """
@@ -62,19 +67,19 @@ process getBag {
  */
 process getData {
   tag "${repRID}"
-  publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.getData.err"
+  publishDir "${logsDir}", mode: "copy", pattern: "*.getData.err"
 
   input:
     path script_bdbagFetch
-    path cookies, stageAs: 'deriva-cookies.txt' from bdbag
+    path cookies, stageAs: "deriva-cookies.txt" from bdbag
     path bagit
 
   output:
     path ("*.R{1,2}.fastq.gz") into fastqs
-    file("**/File.csv") into fileMeta
-    file("**/Experiment Settings.csv") into experimentSettingsMeta
-    file("**/Experiment.csv") into experimentMeta
-    file ("${repRID}.getData.err")
+    path ("**/File.csv") into fileMeta
+    path ("**/Experiment Settings.csv") into experimentSettingsMeta
+    path ("**/Experiment.csv") into experimentMeta
+    path ("${repRID}.getData.err")
 
   script:
     """
@@ -87,14 +92,14 @@ process getData {
     echo "LOG: deriva cookie linked" >>${repRID}.getData.err
     
     # get bagit basename
-    replicate=\$(basename "${bagit}" | cut -d '.' -f1)
+    replicate=\$(basename "${bagit}" | cut -d "." -f1)
     echo "LOG: \${replicate}" >>${repRID}.getData.err
     
     # unzip bagit
     unzip ${bagit} 2>>${repRID}.getData.err
     echo "LOG: replicate bdbag unzipped" >>${repRID}.getData.err
     
-    # bagit fetch fastq's only and rename by repRID
+    # bagit fetch fastq"s only and rename by repRID
     sh ${script_bdbagFetch} \${replicate} ${repRID} 2>>${repRID}.getData.err
     echo "LOG: replicate bdbag fetched" >>${repRID}.getData.err
     """
@@ -105,7 +110,7 @@ process getData {
 */
 process parseMetadata {
   tag "${repRID}"
-  publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.parseMetadata.err"
+  publishDir "${logsDir}", mode: "copy", pattern: "*.parseMetadata.err"
 
   input:
     path script_parseMeta
@@ -115,7 +120,7 @@ process parseMetadata {
     path experimentMeta
 
   output:
-    path 'design.csv' into metadata
+    path "design.csv" into metadata
 
   script:
     """
@@ -135,7 +140,7 @@ process parseMetadata {
     echo "LOG: endedness manually detected: \${endsManual}" >>${repRID}.parseMetadata.err
 
     # Get strandedness metadata
-    stranded=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p stranded)
+    stranded=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p stranded -e \${endsManual})
     echo "LOG: strandedness metadata parsed: \${stranded}" >>${repRID}.parseMetadata.err
     
     # Get spike-in metadata
@@ -146,27 +151,8 @@ process parseMetadata {
     species=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentMeta}" -p species)
     echo "LOG: species metadata parsed: \${species}" >>${repRID}.parseMetadata.err
 
-    #Set the correct Reference Directory
-    if [ "\${spike}" == 'yes' ]; then
-      if [ "\${species}" == 'Homo sapiens' ]; then
-        referenceDir="/project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12-S/hisat2/genome";
-        echo "LOG: Referece set to Homo sapiens with spike-in." >>${repRID}.parseMetadata.err;
-      elif [ "\${species}" == 'Mus musculus' ]; then
-        referenceDir="/project/BICF/BICF_Core/shared/gudmap/references/GRCm38.P6-S/hisat2/genome";
-        echo "LOG: Referece set to Mus musculus with spike-in." >>${repRID}.parseMetadata.err;
-      fi;
-    else
-      if [ "\${species}" == 'Homo sapiens' ]; then
-        referenceDir="/project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome";
-        echo "LOG: Referece set to Homo sapiens without spike-in." >>${repRID}.parseMetadata.err;
-      elif [ "\${species}" == 'Mus musculus' ]; then
-        referenceDir="/project/BICF/BICF_Core/shared/gudmap/references/GRCm38.P6/hisat2/genome";
-        echo "LOG: Referece set to Mus musculus without spike-in." >>${repRID}.parseMetadata.err;
-      fi;
-    fi;
-    
     # Save design file
-    echo "\${rep},\${endsMeta},\${endsManual},\${stranded},\${spike},\${species},\${referenceDir}" > design.csv
+    echo "\${rep},\${endsMeta},\${endsManual},\${stranded},\${spike},\${species}" > design.csv
     """
 }
 
@@ -177,25 +163,71 @@ endsManual = Channel.create()
 stranded = Channel.create()
 spike = Channel.create()
 species = Channel.create()
-referenceDir = Channel.create()
-metadata.splitCsv(sep: ',', header: false).separate(
+metadata.splitCsv(sep: ",", header: false).separate(
   rep,
   endsMeta,
   endsManual,
   stranded,
   spike,
-  species,
-  referenceDir
+  species
 )
 endsManual.into {
   endsManual_trimData
-  endsManual_alignReads
+  endsManual_alignData
 }
 stranded.into {
-  stranded_alignReads
+  stranded_alignData
+}
+spike.into{
+  spike_getRef
+}
+species.into {
+  species_getRef
 }
-referenceDir.into {
-  referenceDir_alignReads
+
+/*
+  * getRef: Dowloads appropriate reference
+*/
+process getRef {
+  tag "${species_getRef}"
+  publishDir "${logsDir}", mode: "copy", pattern: "*.getRef.err"
+
+  input:
+    val referenceBase
+    val refVersion
+    val refMuVersion
+    val refHuVersion
+    val spike_getRef
+    val species_getRef
+
+  output:
+    path ("*")  into reference
+  
+  script:
+    """
+    hostname >>${repRID}.getRef.err
+    ulimit -a >>${repRID}.getRef.err
+    export https_proxy=\${http_proxy}
+
+    # retreive appropriate reference from S3 bucket
+    if [ "${species_getRef}" == "Mus musculus" ]
+    then
+      references=\$(echo ${referenceBase}/mouse/${refVersion}/GRCm${refMuVersion})
+    elif [ '${species_getRef}' == "Homo sapiens" ]
+    then
+      references=\$(echo ${referenceBase}/human/${refVersion}/GRCh${refHuVersion})
+    else
+      exit 1
+    fi
+    if [ "${spike_getRef}" == "yes" ]
+    then
+      references=\$(echo \${reference}-S/)
+    elif [ "${spike_getRef}" == "no" ]
+    then
+      reference=\$(echo \${references}/)
+    fi
+    aws s3 cp "\${references}" ./ --recursive >>${repRID}.getRef.err
+    """
 }
 
 /*
@@ -203,16 +235,16 @@ referenceDir.into {
 */
 process trimData {
   tag "${repRID}"
-  publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.trimData.*"
+  publishDir "${logsDir}", mode: "copy", pattern: "*.trimData.*"
 
   input:
     val endsManual_trimData
-    file(fastq) from fastqs
+    path (fastq) from fastqs
 
   output:
     path ("*.fq.gz") into fastqs_trimmed
-    file ("${repRID}.trimData.log")
-    file ("${repRID}.trimData.err")
+    path ("${repRID}.trimData.log")
+    path ("${repRID}.trimData.err")
 
   script:
     """
@@ -220,32 +252,34 @@ process trimData {
     ulimit -a >>${repRID}.trimData.err
 
     # trim fastqs
-    if [ '${endsManual_trimData}' == 'se' ]
+    if [ "${endsManual_trimData}" == "se" ]
     then
-      trim_galore --gzip -q 25 --illumina --length 35 --basename ${repRID} -j `nproc` ${fastq[0]} 1>>${repRID}.trimData.log 2>>${repRID}.trimData.err;
-    else
-      trim_galore --gzip -q 25 --illumina --length 35 --paired --basename ${repRID} -j `nproc` ${fastq[0]} ${fastq[1]} 1>>${repRID}.trimData.log 2>>${repRID}.trimData.err;
+      trim_galore --gzip -q 25 --illumina --length 35 --basename ${repRID} -j `nproc` ${fastq[0]} 1>>${repRID}.trimData.log 2>>${repRID}.trimData.err
+    elif [ "${endsManual_trimData}" == "pe" ]
+    then
+      trim_galore --gzip -q 25 --illumina --length 35 --paired --basename ${repRID} -j `nproc` ${fastq[0]} ${fastq[1]} 1>>${repRID}.trimData.log 2>>${repRID}.trimData.err
     fi
     """
 }
 
 /*
- * alignReads: aligns the reads to a reference database
+ * alignData: aligns the reads to a reference database
 */
-process alignReads {
+process alignData {
   tag "${repRID}"
-  publishDir "${outDir}/aligned", mode: "copy", pattern: "${repRID}.{unal,sorted}.{gz,bam,bai}"
-  publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.align.{out,err}"
+  publishDir "${logsDir}", mode: "copy", pattern: "*.align.{out,err}"
 
   input:
-    val endsManual_alignReads
-    val stranded_alignReads
-    path fqs from fastqs_trimmed
-    val referenceDir_alignReads
+    val endsManual_alignData
+    val stranded_alignData
+    path fastq from fastqs_trimmed
+    path reference
 
   output:
-    tuple repRID, file ("${repRID}.unal.gz"), file ("${repRID}.sorted.bam"), file ("${repRID}.sorted.bai") into dedupReads
-    tuple repRID, file ("${repRID}.align.out"), file ("${repRID}.align.err")
+    path ("${repRID}.sorted.bam") into rawBam
+    path ("${repRID}.sorted.bai") into rawBai
+    path ("${repRID}.align.out")
+    path ("${repRID}.align.err")
 
   script:
     """
@@ -253,10 +287,15 @@ process alignReads {
     ulimit -a >>${repRID}.align.err
 
     # align reads
-    if [ "${endsManual_alignReads}" == 'pe' ]; then
-    hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x ${referenceDir_alignReads} ${stranded_alignReads} --no-mixed --no-discordant -1 ${fqs[0]} -2 ${fqs[1]} 1>${repRID}.align.out 2>>${repRID}.align.err;
-    else hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x ${referenceDir_alignReads} ${stranded_alignReads} -U ${fqs[0]} 1>${repRID}.align.out 2>>${repRID}.align.err;
-    fi;
+    if [ "${endsManual_alignData}" == "se" ]
+    then
+      hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x hisat2/genome ${stranded_alignData} -U ${fastq[0]} 1>${repRID}.align.out 2>${repRID}.align.err
+    elif [ "${endsManual_alignData}" == "pe" ]
+    then
+      hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x hisat2/genome ${stranded_alignData} --no-mixed --no-discordant -1 ${fastq[0]} -2 ${fastq[1]} 1>${repRID}.align.out 2>${repRID}.align.err
+    fi
+    
+    # convert sam to bam and sort and index
     samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o ${repRID}.bam ${repRID}.sam 1>>${repRID}.align.out 2>>${repRID}.align.err;
     samtools sort -@ `nproc` -O BAM -o ${repRID}.sorted.bam ${repRID}.bam 1>>${repRID}.align.out 2>>${repRID}.align.err;
     samtools index -@ `nproc` -b ${repRID}.sorted.bam ${repRID}.sorted.bai 1>>${repRID}.align.out 2>>${repRID}.align.err;
@@ -266,16 +305,18 @@ process alignReads {
 /*
  *dedupReads: mark the duplicate reads, specifically focused on PCR or optical duplicates
 */
-process dedupReads {
+process dedupData {
   tag "${repRID}"
-  publishDir "${outDir}/deduped", mode: 'copy', pattern: "${repRID}.deduped.{bam,Metrics.txt}"
-  publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.dedup.{out,err}"
+  publishDir "${outDir}/bam", mode: 'copy', pattern: "*.deduped.bam"
+  publishDir "${logsDir}", mode: 'copy', pattern: "*.dedup.{out,err}"
 
   input:
-    tuple repRID, file (unal), file (sortedBam), file (sortedBai) from dedupReads
+    path rawBam
 
   output:
-    tuple repRID, file ("${repRID}.deduped.bam"), file ("${repRID}.deduped.Metrics.txt")
+    path ("${repRID}.deduped.bam") into dedupBam
+    path ("${repRID}.dedup.out")
+    path ("${repRID}.dedup.err")
 
   script:
     """
@@ -283,6 +324,6 @@ process dedupReads {
     ulimit -a >>${repRID}.dedup.err
 
     #Remove duplicated reads
-    java -jar /picard/build/libs/picard.jar MarkDuplicates I=${sortedBam} O=${repRID}.deduped.bam M=${repRID}.deduped.Metrics.txt REMOVE_DUPLICATES=true 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
+    java -jar /picard/build/libs/picard.jar MarkDuplicates I=${rawBam} O=${repRID}.deduped.bam M=${repRID}.deduped.Metrics.txt REMOVE_DUPLICATES=true 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
     """
-}
+}
\ No newline at end of file
diff --git a/workflow/scripts/modifyFetch.py b/workflow/scripts/modifyFetch.py
deleted file mode 100644
index e6accfbbaee5ac303253294f69f8f345c7ba1dc5..0000000000000000000000000000000000000000
--- a/workflow/scripts/modifyFetch.py
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-import pandas as pd
-import re
-
-def get_args():
-    parser = argparse.ArgumentParser()
-    parser.add_argument('-f', '--files',help="The fetch file from bdgap.zip.",required=True)
-    args = parser.parse_args()
-    return args
-
-def main():
-    args = get_args()
-    fetchFile = pd.read_csv(args.files+"/fetch.txt",sep="\t",header=None)
-    fileFile = pd.read_csv(args.files+"/data/File.csv",sep=",",header=0)
-    fileFile_filtered = fileFile[fileFile["File_Type"]=="FastQ"]
-    fetchFile_filtered = fetchFile[fetchFile[2].str[-9:]==".fastq.gz"]
-    fetchFile_filtered_renamed = fetchFile_filtered
-    for i in fileFile_filtered["File_Name"]:
-        fetchFile_filtered_renamed[2][fetchFile_filtered_renamed[2].str.contains(i,regex=False)] = fetchFile_filtered_renamed[2][fetchFile_filtered_renamed[2].str.contains(i,regex=False)].values[0].replace(re.sub("\.R.\.fastq\.gz","",i),fileFile_filtered["Replicate_RID"][fileFile_filtered["File_Name"]==i].values[0])
-    fetchFile_filtered_renamed.to_csv(args.files+"/fetch.txt",sep="\t",header=False,index=False)
-
-if __name__ == '__main__':
-    main()
\ No newline at end of file
diff --git a/workflow/scripts/parseMeta.py b/workflow/scripts/parseMeta.py
index 4797610f870f8e8f22024e0198dc0255c0829073..eaa2656f9266a5c3de07fb0fc80ad5aeb2ea8422 100644
--- a/workflow/scripts/parseMeta.py
+++ b/workflow/scripts/parseMeta.py
@@ -10,6 +10,7 @@ def get_args():
     parser.add_argument('-r', '--repRID',help="The replicate RID.",required=True)
     parser.add_argument('-m', '--metaFile',help="The metadata file to extract.",required=True)
     parser.add_argument('-p', '--parameter',help="The parameter to extract.",required=True)
+    parser.add_argument('-e', '--endsManual',help="The endness.",required=False)
     args = parser.parse_args()
     return args
 
@@ -55,9 +56,9 @@ def main():
     # Get strandedness metadata from 'Experiment Settings.csv'
     if (args.parameter == "stranded"):
         if (metaFile.Has_Strand_Specific_Information.unique() == "yes"):
-            if endsManual == "se":
+            if (args.endsManual=="se"):
                 stranded = "--rna-strandness F"
-            else:
+            elif (args.endsManual=="pe"):
                 stranded = "--rna-strandness FR"
         elif (metaFile.Has_Strand_Specific_Information.unique() == "no"):
             stranded = ""
diff --git a/workflow/scripts/splitFetch.py b/workflow/scripts/splitFetch.py
deleted file mode 100644
index 63385c184ff7bd6ddb4cb047c81a693cf7a8ecfb..0000000000000000000000000000000000000000
--- a/workflow/scripts/splitFetch.py
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-import pandas as pd
-import os
-
-def get_args():
-    parser = argparse.ArgumentParser()
-    parser.add_argument('-f', '--files',help="The fetch file from bdgap.zip.",required=True)
-    args = parser.parse_args()
-    return args
-
-def main():
-    args = get_args()
-    fetchFile = pd.read_csv(args.files+"/fetch.txt",sep="\t",header=None)
-    fileFile = pd.read_csv(args.files+"/data/File.csv",sep=",",header=0)
-    replicateRID = fileFile.Replicate_RID.unique()
-    fetchArray = {i:fileFile.URI[(fileFile.Replicate_RID == i) & (fileFile.File_Type == "FastQ")] for i in replicateRID}
-    for i in replicateRID:
-        if not os.path.exists(i):
-            os.mkdir("Replicate_"+i)
-        fetchFile[fetchFile[0].str.contains('|'.join(fetchArray[i]))].to_csv("Replicate_"+i+"/fetch.txt",sep="\t",header=False,index=False)
-
-if __name__ == '__main__':
-    main()
\ No newline at end of file
diff --git a/workflow/tests/test_alignReads.py b/workflow/tests/test_alignReads.py
index 79770bb42245df6da0ce7fa1081d78ec5aed736f..d95e63a6426e5d1cbec874b0c4e86b17388ba975 100644
--- a/workflow/tests/test_alignReads.py
+++ b/workflow/tests/test_alignReads.py
@@ -7,39 +7,17 @@ import utils
 
 data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 	'/../../'
-logs_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-	'/../../'
 
 
 @pytest.mark.alignData
 def test_alignData_se():
-	assert os.path.exists(os.path.join(data_output_path, '16-1ZX4.unal.gz'))
-	assert utils.count_lines(os.path.join(data_output_path, '16-1ZX4.unal.gz')) == 3070528
-	assert os.path.exists(os.path.join(data_output_path, '16-1ZX4.sorted.bam'))
-	assert os.path.exists(os.path.join(data_output_path, '16-1ZX4.sorted.bai'))
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.unal.gz'))
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.bam'))
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.sorted.bai'))
 
 
 @pytest.mark.alignData
 def test_alignData_pe():
-	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA.unal.gz'))
-	assert utils.count_lines(os.path.join(data_output_path, 'Q-Y5JA.unal.gz')) == 0
-	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA.sorted.bam'))
-	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA.sorted.bai'))
-
-
-@pytest.mark.alignLogs
-def test_alignLogs_se():
-	assert os.path.exists(os.path.join(logs_output_path, '16-1ZX4.align.err'))
-	assert utils.count_lines(os.path.join(logs_output_path, '16-1ZX4.align.err')) == 7
-	assert '34497376 reads; of these:' in open(os.path.join(logs_output_path, '16-1ZX4.align.err')).readlines()[0]
-	assert os.path.exists(os.path.join(logs_output_path, '16-1ZX4.align.out'))
-	assert utils.count_lines(os.path.join(logs_output_path, '16-1ZX4.align.out')) == 0
-
-
-@pytest.mark.alignLogs
-def test_alignLogs_pe():
-	assert os.path.exists(os.path.join(logs_output_path, 'Q-Y5JA.align.err'))
-	assert utils.count_lines(os.path.join(logs_output_path, 'Q-Y5JA.align.err')) == 7
-	assert '15824858 reads; of these:' in open(os.path.join(logs_output_path, 'Q-Y5JA.align.err')).readlines()[0]
-	assert os.path.exists(os.path.join(logs_output_path, 'Q-Y5JA.align.out'))
-	assert utils.count_lines(os.path.join(logs_output_path, 'Q-Y5JA.align.out')) == 0
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.pe.unal.gz'))
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.pe.sorted.bam'))
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.pe.sorted.bai'))
\ No newline at end of file
diff --git a/workflow/tests/test_dedupReads.py b/workflow/tests/test_dedupReads.py
index e204317e7a30bc05206d64535472963f35da0b5f..0c0cd7aa67ab0e47168f8bf438191f6a9c217b72 100644
--- a/workflow/tests/test_dedupReads.py
+++ b/workflow/tests/test_dedupReads.py
@@ -7,27 +7,8 @@ import utils
 
 data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 	'/../../'
-logs_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-	'/../../'
-
 
-@pytest.mark.dedupData
-def test_dedupData_se():
-	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.deduped.bam'))
-	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.deduped.Metrics.txt'))
 
 @pytest.mark.dedupData
-def test_dedupData_pe():
-	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.pe.deduped.bam'))
-	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.pe.deduped.Metrics.txt'))
-
-
-@pytest.mark.dedupLogs
-def test_dedupLogs_se():
-	assert os.path.exists(os.path.join(logs_output_path, '16-1ZX4.dedup.err'))
-	assert os.path.exists(os.path.join(logs_output_path, '16-1ZX4.dedup.out'))
-
-@pytest.mark.dedupLogs
-def test_dedupLogs_pe():
-	assert os.path.exists(os.path.join(logs_output_path, 'Q-Y5JA.dedup.err'))
-	assert os.path.exists(os.path.join(logs_output_path, 'Q-Y5JA.dedup.out'))
+def test_dedupData():
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.deduped.bam'))
\ No newline at end of file
diff --git a/workflow/tests/test_trimData.py b/workflow/tests/test_trimData.py
index 6538a0081aaea69c5814d479751455abd879f4bc..a8f479afec7b0c97847179f5b7817987ee872a16 100644
--- a/workflow/tests/test_trimData.py
+++ b/workflow/tests/test_trimData.py
@@ -10,9 +10,10 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 
 @pytest.mark.trimData
 def test_trimData_se():
-    assert os.path.exists(os.path.join(test_output_path, '16-1ZX4_trimmed.fq.gz'))
+    assert os.path.exists(os.path.join(test_output_path, 'Q-Y5JA_1M.se_trimmed.fq.gz'))
+
 
 @pytest.mark.trimData
 def test_trimData_pe():
-    assert os.path.exists(os.path.join(test_output_path, 'Q-Y5JA_R1_val_1.fq.gz'))
-    assert os.path.exists(os.path.join(test_output_path, 'Q-Y5JA_R2_val_2.fq.gz'))
\ No newline at end of file
+    assert os.path.exists(os.path.join(test_output_path, 'Q-Y5JA_1M.pe_R1_val_1.fq.gz'))
+    assert os.path.exists(os.path.join(test_output_path, 'Q-Y5JA_1M.pe_R2_val_2.fq.gz'))
\ No newline at end of file