diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 9688452..3c2bccd 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -9,33 +9,35 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       -
         name: Sanitize Repo Name for Tagging
         run: echo ${{ github.repository }} | tr '[:upper:]' '[:lower:]' | (read; echo REPO_LOWER=$REPLY) >> $GITHUB_ENV
       - 
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v2
       - 
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v2
       - 
         name: Login to Docker Hub
-        uses: docker/login-action@v1 
+        uses: docker/login-action@v2
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       - 
         name: Login to GitHub Container Registry
-        uses: docker/login-action@v1
+        uses: docker/login-action@v2
         with:
           registry: ghcr.io
           username: ${{ secrets.GH_USERNAME }}
           password: ${{ secrets.GH_TOKEN }}
       - name: Build and Push
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v4
         with:
           push: true
           tags: |
             ghcr.io/${{ env.REPO_LOWER }}:${{ github.event.release.tag_name }}
+            ghcr.io/${{ env.REPO_LOWER }}:latest
             ${{ env.REPO_LOWER }}:${{ github.event.release.tag_name }}
+            ${{ env.REPO_LOWER }}:latest
diff --git a/.github/workflows/docker_branches.yml b/.github/workflows/docker_branches.yml
index d701a1f..ab756c2 100644
--- a/.github/workflows/docker_branches.yml
+++ b/.github/workflows/docker_branches.yml
@@ -2,7 +2,7 @@ name: Publish Docker image
 on:
   push:
     branches-ignore:
-    - 'master'
+    - 'main'
 
 jobs:
   push_to_registry:
@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       -
         name: Sanitize Repo Name for Tagging
         run: echo ${{ github.repository }} | tr '[:upper:]' '[:lower:]' | (read; echo REPO_LOWER=$REPLY) >> $GITHUB_ENV
@@ -25,18 +25,18 @@ jobs:
             type=ref,event=pr
       - 
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v2
       - 
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v2
       - 
         name: Login to Docker Hub
-        uses: docker/login-action@v1 
+        uses: docker/login-action@v2
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       - name: Push to Docker Hub
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v4
         with:
           push: true
           tags: ${{ steps.meta.outputs.tags }}
diff --git a/.github/workflows/lint-check.yml b/.github/workflows/lint-check.yml
index 946a9f0..d4dbfc9 100644
--- a/.github/workflows/lint-check.yml
+++ b/.github/workflows/lint-check.yml
@@ -3,49 +3,40 @@ name: lint-check
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
     branches:
-      - master
+      - main
 
 jobs:
   import_syntax_check:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Check import syntax
       run: |
         EXITCODE=0
         for file in $(find . -name '*.wdl'); do
           >&2 echo "Checking file $file..."
           import_lines=$(awk '/import/' "$file")
-          bad_lines=$(echo "$import_lines" | awk '!/https:\/\/raw.githubusercontent.com\/stjude\/xenocp\/master/ && !/https:\/\/raw.githubusercontent.com\/stjudecloud\/workflows\/master/' | grep -v '# lint-check: ignore') || true
+
+          bad_lines=$(echo "$import_lines" | awk '/https:\/\/raw.githubusercontent.com\/stjude\/XenoCP/') || true
           if [ -n "$bad_lines" ]; then
-            >&2 echo "Must import files from the master branch on Github."
+            >&2 echo "Imports from this repo must use relative paths!"
             >&2 echo "The following lines are bad:"
             >&2 echo "$bad_lines"
             >&2 echo ""
             EXITCODE=1
           fi
-        done
-        exit $EXITCODE
-  docker_pull_check:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - name: Ensure SemVer'd docker images are being pulled
-      run: |
-        EXITCODE=0
-        files=$(find . -name '*.wdl')
-        for file in $files; do
-          while IFS= read -r line; do
-            tag=$(echo "$line" | awk -F ':' '{print substr($3, 1, length($3)-1)}')
-            if ! [[ $tag =~ ^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(-(0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(\.(0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*)?(\+[0-9a-zA-Z-]+(\.[0-9a-zA-Z-]+)*)?$ ]]; then
-              >&2 echo "All Docker containers must be using an official SemVer tagged image"
-              >&2 echo "Offending line: $line"
-              >&2 echo "In file: $file"
-              EXITCODE=1
-            fi
-          done < <(awk '/docker: .*stjudecloud/ || /docker: .*stjude/' < "$file")
+
+          bad_lines=$(echo "$import_lines" | awk '/http/ && (/main/ || /master/)') || true
+          if [ -n "$bad_lines" ]; then
+            >&2 echo "Imports from external repos must use a tagged release!"
+            >&2 echo "The following lines are bad:"
+            >&2 echo "$bad_lines"
+            >&2 echo ""
+            EXITCODE=1
+          fi
+
         done
         exit $EXITCODE
diff --git a/.github/workflows/miniwdl-check.yml b/.github/workflows/miniwdl-check.yml
index 71af5a2..ff51b75 100644
--- a/.github/workflows/miniwdl-check.yml
+++ b/.github/workflows/miniwdl-check.yml
@@ -6,11 +6,11 @@ jobs:
   miniwdl_check:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
-        python-version: '3.6'
+        python-version: '3.10'
     - name: Install miniwdl
       run: |
         python -m pip install --upgrade pip
@@ -20,10 +20,7 @@ jobs:
         EXITCODE=0
         echo "Checking WDL files using \`miniwdl check\`."
         files=$(find . -name '*.wdl')
-        for file in $files; do
-          sed -i 's,https://raw.githubusercontent.com/stjude/xenocp/'"$(echo ${GITHUB_REF#refs/heads/})"','"$(pwd)"',g' "$file"
-          sed -i 's,https://raw.githubusercontent.com/stjude/xenocp/master,'"$(pwd)"',g' "$file"
-        done
+
         for file in $files; do
           echo "  [***] $file [***]"
           miniwdl check "$file"
diff --git a/.github/workflows/release-check.yml b/.github/workflows/release-check.yml
new file mode 100644
index 0000000..d836a76
--- /dev/null
+++ b/.github/workflows/release-check.yml
@@ -0,0 +1,31 @@
+name: release-check
+
+on:
+  push:
+    branches:
+      - release
+  pull_request:
+    branches:
+      - release
+
+jobs:
+  docker_pull_check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Ensure SemVer'd docker images are being pulled
+      run: |
+        EXITCODE=0
+        files=$(find . -name '*.wdl')
+        for file in $files; do
+          while IFS= read -r line; do
+            tag=$(echo "$line" | awk -F ':' '{print substr($3, 1, length($3)-1)}')
+            if ! [[ $tag =~ ^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(-(0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(\.(0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*)?(\+[0-9a-zA-Z-]+(\.[0-9a-zA-Z-]+)*)?$ ]]; then
+              >&2 echo "All Docker containers must be using an official SemVer tagged image"
+              >&2 echo "Offending line: $line"
+              >&2 echo "In file: $file"
+              EXITCODE=1
+            fi
+          done < <(awk '/docker: .*stjudecloud/ || /docker: .*stjude/' < "$file")
+        done
+        exit $EXITCODE
diff --git a/Dockerfile b/Dockerfile
index c42d6ac..53c4712 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,6 @@
-FROM ubuntu:18.04 as builder
+FROM ubuntu:20.04 as builder
+
+ARG DEBIAN_FRONTEND=noninteractive
 
 RUN apt-get update \
     && apt-get --yes install \
@@ -73,7 +75,7 @@ RUN cd /tmp/xenocp \
     && gradle installDist \
     && cp -r build/install/xenocp /opt
 
-FROM ubuntu:18.04
+FROM ubuntu:20.04
 
 RUN apt-get update \
     && apt-get --yes install --no-install-recommends \
@@ -82,6 +84,7 @@ RUN apt-get update \
         openjdk-11-jre-headless \
         python3 \
         python3-distutils \
+        python-is-python3 \
         file \
     && rm -rf /var/lib/apt/lists/*
 
@@ -98,4 +101,4 @@ COPY --from=builder /opt/xenocp/bin/* /usr/local/bin/
 
 COPY cwl /opt/xenocp/cwl
 
-ENTRYPOINT ["cwl-runner", "--parallel", "--outdir", "results", "/opt/xenocp/cwl/xenocp.cwl"]
+ENTRYPOINT ["cwl-runner", "--parallel", "--outdir", "results", "--no-container", "/opt/xenocp/cwl/xenocp.cwl"]
diff --git a/RELEASE.md b/RELEASE.md
new file mode 100644
index 0000000..b6f74b8
--- /dev/null
+++ b/RELEASE.md
@@ -0,0 +1,5 @@
+# Release
+
+  * [ ] Update version in `dx_app/dxapp.json`.
+  * [ ] Update `wdl/tools/xenocp.wdl` with version.
+  * [ ] Update `wdl/workflows/xenocp.wdl` with version.
diff --git a/bin/picard b/bin/picard
new file mode 100755
index 0000000..fea6036
--- /dev/null
+++ b/bin/picard
@@ -0,0 +1,2 @@
+#!/usr/bin/env bash
+java -jar /opt/picard/lib/picard*.jar "$@"
diff --git a/cwl/bwa_mem_onlymapped.cwl b/cwl/bwa_mem_onlymapped.cwl
index 71f3a69..1e9db9d 100644
--- a/cwl/bwa_mem_onlymapped.cwl
+++ b/cwl/bwa_mem_onlymapped.cwl
@@ -12,6 +12,11 @@ hints:
       tweak_sam:
         specs: ["java.sh org.stjude.compbio.sam.TweakSam"]
 
+requirements:
+  ResourceRequirement:
+    ramMin: 15000
+    coresMin: 1
+
 inputs:
   ref_db_prefix: 
     type: string
diff --git a/cwl/cat.cwl b/cwl/cat.cwl
new file mode 100644
index 0000000..87dd395
--- /dev/null
+++ b/cwl/cat.cwl
@@ -0,0 +1,32 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+doc: |
+  Merge a set of files into file using the cat utility.
+
+requirements:
+ - class: InlineJavascriptRequirement
+
+baseCommand: cat
+
+inputs:
+  output_file:
+    type: string
+    doc: |
+      Name of final file.
+
+  input_files:
+    type: File[]
+    inputBinding:
+      position: 4
+    doc: |
+      Array of files to merge. 
+
+stdout: $(inputs.output_file)
+
+outputs:
+  combined_file:
+    type: File
+    outputBinding:
+      glob: $(inputs.output_file)
\ No newline at end of file
diff --git a/cwl/xenocp.cwl b/cwl/xenocp.cwl
index 618c553..b741354 100755
--- a/cwl/xenocp.cwl
+++ b/cwl/xenocp.cwl
@@ -10,7 +10,7 @@ requirements:
   - class: SubworkflowFeatureRequirement
 
 inputs:
-  bam: 
+  bam:
     type: File
     label: Aligned sequences in BAM format
     secondaryFiles:
@@ -19,7 +19,7 @@ inputs:
     type: string
     label: contamination genome reference db prefix
   aligner:
-    type: 
+    type:
       type: enum
       symbols: ["bwa aln", "bwa mem", "star"]
       name: aligner
@@ -39,7 +39,7 @@ inputs:
   output_extension:
     type: string?
     default: bam
-  n_threads: 
+  n_threads:
     type: int?
     default: 1
 
@@ -51,31 +51,27 @@ outputs:
     type: File
     outputSource: finish/flagstat
   contam_list:
-    type:
-      type: array
-      items: File
-    outputSource: contamination/contam_list
+    type: File
+    outputSource: merge_contam_list/combined_file
   output_tie_bam:
-    type:
-      type: array
-      items: File
-    outputSource: contamination/output_tie_bam
+    type: File
+    outputSource: merge_tie_bam/final_bam
 
 steps:
   # Step01: extract chromosome information from input bam
   split:
     run: extract.cwl
-    in: 
+    in:
       bam: bam
     out: [split_bams, unmapped]
-  
+
   # Step02: extract mapped reads and convert to fastq
   mapped-fastq:
     run: view_awk_picard.cwl
     in:
-      input_bam: 
+      input_bam:
         source: split/split_bams
-        linkMerge: merge_flattened 
+        linkMerge: merge_flattened
       output_fastq:
         valueFrom: $(inputs.input_bam.nameroot).fastq   # here "inputs" refers to inputs in view_awk_picard.cwl
     scatter: [input_bam]
@@ -114,7 +110,7 @@ steps:
       ResourceRequirement:
         ramMin: 4800
         coresMin: 1
-  
+
   # Step03c: map extracted reads to the contamination genome with STAR
   mapping-star:
     run: star_onlymapped.cwl
@@ -137,25 +133,25 @@ steps:
     run: create_contam_lists.cwl
     in:
       input_bam:
-        source: split/split_bams 
-      output_contam_list: 
+        source: split/split_bams
+      output_contam_list:
         valueFrom: $(inputs.input_bam.nameroot).contam.txt
       tie_bam:
         valueFrom: $(inputs.input_bam.nameroot).tie.bam
-      contam_bams: 
+      contam_bams:
         source: [mapping-bwa-aln/bam, mapping-bwa-mem/bam, mapping-star/bam]
         linkMerge: merge_flattened
         pickValue: all_non_null
     scatter: [input_bam, contam_bams]
     scatterMethod: dotproduct
     out: [contam_list, output_tie_bam]
-  
-  # Step05: clean the original bam by setting the contamination reads to be unmapped
+
+  # Step05a: clean the original bam by setting the contamination reads to be unmapped
   cleanse:
     run: tweak_sam.cwl
     in:
-      input_bam: 
-        source: split/split_bams 
+      input_bam:
+        source: split/split_bams
       output_bam:
         valueFrom: $(inputs.input_bam.nameroot).cleaned.bam
       unmap_reads: contamination/contam_list
@@ -163,11 +159,24 @@ steps:
     scatterMethod: dotproduct
     out: [cleaned_bam]
 
-  # Step06: merge split bams, index and mark duplicates
+  # Step05b: sort tie BAMs prior to merge
+  sort-bams:
+    run: bio-cwl-tools:picard/picard_SortSam.cwl
+    in:
+      alignments: contamination/output_tie_bam
+      sort_order:
+        valueFrom: $("coordinate")
+      validation_stringency:
+        valueFrom: $("SILENT")
+    scatter: [alignments]
+    scatterMethod: dotproduct
+    out: [sorted_alignments]
+
+  # Step06a: merge split bams, index and mark duplicates
   finish:
     run: merge_markdup_index.cwl
     in:
-      input_bams: 
+      input_bams:
         source: [cleanse/cleaned_bam, split/unmapped]
         linkMerge: merge_flattened
       output_bam:
@@ -175,8 +184,33 @@ steps:
         valueFrom: ${return self.nameroot + ".xenocp.bam"}
       n_threads: n_threads
     out: [final_bam, flagstat]
-  
-  # Step07: QC the merged bam
+
+  # Step06b: merge tie bams and index
+  merge_tie_bam:
+    run: merge_markdup_index.cwl
+    in:
+      input_bams:
+        source: [cleanse/cleaned_bam, split/unmapped]
+        linkMerge: merge_flattened
+      output_bam:
+        source: bam
+        valueFrom: ${return self.nameroot + ".xenocp.tie.bam"}
+      n_threads: n_threads
+      skip_dup:
+        valueFrom: $(true)
+    out: [final_bam, flagstat]
+
+  # Step07: Combine contam lists
+  merge_contam_list:
+    run: cat.cwl
+    in:
+      input_files: contamination/contam_list
+      output_file:
+        source: bam
+        valueFrom: ${return self.nameroot + ".contam.txt"}
+    out: [combined_file]
+
+  # Step08: QC the merged bam
   finalqc:
     run: qc_bam.cwl
     in:
@@ -201,6 +235,7 @@ doc: |
 
 $namespaces:
   s: http://schema.org/
+  bio-cwl-tools: https://raw.githubusercontent.com/common-workflow-library/bio-cwl-tools/release/
 
 $schemas:
  - https://schema.org/version/latest/schemaorg-current-https.rdf
diff --git a/dependencies/lib/java/xenocp-dependencies.jar b/dependencies/lib/java/xenocp-dependencies.jar
index 8ba7897..c6b43e5 100755
Binary files a/dependencies/lib/java/xenocp-dependencies.jar and b/dependencies/lib/java/xenocp-dependencies.jar differ
diff --git a/dx_app/dxapp.json b/dx_app/dxapp.json
index ee9edbb..0d3e5b1 100644
--- a/dx_app/dxapp.json
+++ b/dx_app/dxapp.json
@@ -3,7 +3,7 @@
   "title": "XenoCP (St. Jude)",
   "summary": "Xenograft sample cleaning pipeline",
   "dxapi": "1.0.0",
-  "version": "3.1.4",
+  "version": "4.0.0-alpha",
   "openSource": true,
   "developers": ["user-lding", "user-mrusch", "user-athrashe"],
   "authorizedUsers": [
@@ -46,7 +46,7 @@
       "name": "ref_name",
       "label": "Host Genome",
       "class": "string",
-      "choices": ["GRCm38", "MGSCv37", "Custom, specified as input"],
+      "choices": ["GRCm39", "GRCm38", "MGSCv37", "Custom, specified as input"],
       "optional": false,
       "default": "GRCm38",
       "help": ""
@@ -118,7 +118,10 @@
   ],
   "billTo": "org-stjude_cloud",
   "access": {
-    "allProjects": "VIEW"
+    "allProjects": "VIEW",
+    "network": [
+      "*"
+    ]
   },
   "runSpec": {
     "timeoutPolicy": {
diff --git a/dx_app/src/stjude_xenocp.sh b/dx_app/src/stjude_xenocp.sh
index e95055e..0b095f4 100644
--- a/dx_app/src/stjude_xenocp.sh
+++ b/dx_app/src/stjude_xenocp.sh
@@ -70,7 +70,7 @@ main() {
         dx download -o $local_reference_dir -r project-F5444K89PZxXjBqVJ3Pp79B4:/global/reference/Mus_musculus/$ref_name/BWA
         mv $local_reference_dir/BWA/* $local_reference_dir/
       else
-        dx download -o $local_reference_dir -r project-FzJ7yx89Q0f0pBj5P2j1g0vB:/$ref_name/STAR
+        dx download -o $local_reference_dir -r project-F5444K89PZxXjBqVJ3Pp79B4:/global/reference/Mus_musculus/$ref_name/STAR
         reference_prefix="STAR"
       fi
     else
@@ -112,13 +112,6 @@ output_extension: $output_extension
 aligner: $aligner
 EOF
 
-    echo "  [*] Loading container image ..."
-    image_tarfile_path=/stjude/xenocp-docker.tar
-    if [ -e $image_tarfile_path.gz ]
-    then gunzip $image_tarfile_path.gz
-    fi
-    docker load -i $image_tarfile_path
-    
     echo "=== Execution ==="
     
     # Don't make assumptions about the tag that was used when the image was
@@ -133,9 +126,10 @@ EOF
       --mount type=bind,source=$local_data_dir,target=$container_data_dir,readonly \
       --mount type=bind,source=$local_reference_dir,target=$container_reference_dir,readonly \
       --mount type=bind,source=$local_output_dir,target=$container_output_dir \
-      $image_id \
+      ghcr.io/stjude/xenocp:3.1.4 \
       $container_data_dir/inputs.yml
 
+
     echo "=== Wrap Up ==="
     echo "  [*] Uploading outputs ..."
     mv -v $local_output_dir/*.xenocp.bam* $local_output_dir/output_bam
diff --git a/wdl/tools/xenocp.wdl b/wdl/tools/xenocp.wdl
index d1e2232..fdbde52 100644
--- a/wdl/tools/xenocp.wdl
+++ b/wdl/tools/xenocp.wdl
@@ -35,7 +35,7 @@ task get_chroms {
         memory: memory_gb + " GB"
         disk: disk_size + " GB"
         cpu: ncpu
-        docker: 'stjude/xenocp:3.1.4'
+        docker: 'ghcr.io/stjude/xenocp:4.0.0-alpha'
         maxRetries: max_retries
     }
 
@@ -59,7 +59,7 @@ task extract_mismatch {
     input {
         File input_bam
         File input_bai
-        Int memory_gb = 1
+        Int memory_gb = 2
         Int? disk_size_gb
         Int max_retries = 1
     }
@@ -78,7 +78,7 @@ task extract_mismatch {
         memory: memory_gb + " GB"
         disk: disk_size + " GB"
         cpu: 1
-        docker: 'stjude/xenocp:3.1.4'
+        docker: 'ghcr.io/stjude/xenocp:4.0.0-alpha'
         maxRetries: max_retries
     }
 
@@ -103,7 +103,7 @@ task extract_by_chrom {
         File input_bam
         File input_bai
         String chromosome
-        Int memory_gb = 1
+        Int memory_gb = 8
         Int? disk_size_gb
         Int max_retries = 1
     }
@@ -122,7 +122,7 @@ task extract_by_chrom {
         memory: memory_gb + " GB"
         disk: disk_size + " GB"
         cpu: 1
-        docker: 'stjude/xenocp:3.1.4'
+        docker: 'ghcr.io/stjude/xenocp:4.0.0-alpha'
         maxRetries: max_retries
     }
 
@@ -175,7 +175,7 @@ task extract_unmapped {
         memory: memory_gb + " GB"
         disk: disk_size + " GB"
         cpu: ncpu
-        docker: 'stjude/xenocp:3.1.4'
+        docker: 'ghcr.io/stjude/xenocp:4.0.0-alpha'
         maxRetries: max_retries
     }
 
@@ -217,7 +217,7 @@ task mapped_fastq {
         memory: memory_gb + " GB"
         disk: disk_size + " GB"
         cpu: 1
-        docker: 'stjude/xenocp:3.1.4'
+        docker: 'ghcr.io/stjude/xenocp:4.0.0-alpha'
         maxRetries: max_retries
     }
 
@@ -240,13 +240,13 @@ task mapped_fastq {
 task create_contam_list {
     input {
         File input_bam
-        String output_contam_list = basename(input_bam, ".bam") + "contam.txt"
+        String output_contam_list = basename(input_bam, ".bam") + ".contam.txt"
         String tie_bam = basename(input_bam, ".bam") + ".tie.bam"
         File contam_bam
         String stringency = "SILENT"
         Int? disk_size_gb
         Int max_retries = 1
-        Int memory_gb = 1
+        Int memory_gb = 2
     }
 
     Float input_bam_size = size(input_bam, "GiB")
@@ -262,7 +262,7 @@ task create_contam_list {
         memory: memory_gb + " GB"
         disk: disk_size + " GB"
         cpu: 1
-        docker: 'stjude/xenocp:3.1.4'
+        docker: 'ghcr.io/stjude/xenocp:4.0.0-alpha'
         maxRetries: max_retries
     }
 
@@ -295,7 +295,7 @@ task cleanse {
         String stringency = "SILENT"
         Int? disk_size_gb
         Int max_retries = 1
-        Int memory_gb = 1
+        Int memory_gb = 7
     }
 
     Float input_bam_size = size(input_bam, "GiB")
@@ -311,7 +311,7 @@ task cleanse {
         memory: memory_gb + " GB"
         disk: disk_size + " GB"
         cpu: 1
-        docker: 'stjude/xenocp:3.1.4'
+        docker: 'ghcr.io/stjude/xenocp:4.0.0-alpha'
         maxRetries: max_retries
     }
 
@@ -361,7 +361,7 @@ task merge_markdup_index {
         memory: memory_gb + " GB"
         disk: disk_size + " GB"
         cpu: 1
-        docker: 'stjude/xenocp:3.1.4'
+        docker: 'ghcr.io/stjude/xenocp:4.0.0-alpha'
         maxRetries: max_retries
     }
 
@@ -409,7 +409,7 @@ task qc {
         memory: memory_gb + " GB"
         disk: disk_size + " GB"
         cpu: ncpu
-        docker: 'stjude/xenocp:3.1.4'
+        docker: 'ghcr.io/stjude/xenocp:4.0.0-alpha'
         maxRetries: max_retries
     }
 
@@ -426,3 +426,44 @@ task qc {
         input_bam: "Input BAM file"
     }
 }
+
+task combine_files {
+    input {
+        Array[File] input_files
+        String output_file
+        Int? disk_size_gb
+        Int max_retries = 1
+        Int memory_gb = 1
+    }
+
+    Float input_file_size = size(input_files, "GiB")
+    Int disk_size = select_first([disk_size_gb, ceil(input_file_size * 2)])
+
+    command <<<
+        set -euo pipefail
+
+        cat ~{sep=" " input_files} > ~{output_file}
+    >>>
+
+    runtime {
+        memory: memory_gb + " GB"
+        disk: disk_size + " GB"
+        cpu: 1
+        docker: 'ghcr.io/stjude/xenocp:4.0.0-alpha'
+        maxRetries: max_retries
+    }
+
+    output {
+        File final_file = output_file
+    }
+
+    meta {
+        author: "Andrew Thrasher"
+        email: "andrew.thrasher@stjude.org"
+        description: "This WDL tool takes a set of files and combines them with the cat utility." 
+    }
+
+    parameter_meta {
+        input_files: "Input files to combine with cat"
+    }
+}
diff --git a/wdl/workflows/xenocp.wdl b/wdl/workflows/xenocp.wdl
index cc27a6b..ae02ddf 100644
--- a/wdl/workflows/xenocp.wdl
+++ b/wdl/workflows/xenocp.wdl
@@ -27,10 +27,10 @@
 
 version 1.0
 
-import "https://raw.githubusercontent.com/stjude/xenocp/3.1.4/wdl/tools/xenocp.wdl" as xenocp_tools
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/bwa.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/star.wdl"
-import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v3.0.0/tools/picard.wdl"
+import "../tools/xenocp.wdl" as xenocp_tools
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v4.0.0-alpha/tools/bwa.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v4.0.0-alpha/tools/star.wdl"
+import "https://raw.githubusercontent.com/stjudecloud/workflows/rnaseq-standard/v4.0.0-alpha/tools/picard.wdl"
 
 workflow xenocp {
     input {
@@ -49,8 +49,9 @@ workflow xenocp {
         aligner: "Which aligner to use to map reads to the host genome to detect contamination: [bwa aln, bwa mem, star]"
         skip_duplicate_marking: "If true, duplicate marking will be skipped when the cleaned BAMs are merged"
     }
-
-    String name = basename(input_bam, ".bam") + ".xenocp.bam"
+    
+    String name = basename(input_bam, ".bam")
+    String output_name = name + ".xenocp.bam"
 
     call xenocp_tools.get_chroms { input: input_bam=input_bam, ncpu=n_threads }
     call xenocp_tools.extract_mismatch as mismatch { input: input_bam=input_bam, input_bai=input_bai }
@@ -71,7 +72,7 @@ workflow xenocp {
     }
     if (aligner == "bwa mem") {
         scatter (fastq in mapped_fastq.fastq){
-            call bwa.bwa_mem as bwa_mem_align { input: fastq=fastq, bwadb_tar_gz=reference_tar_gz, ncpu=n_threads }
+            call bwa.bwa_mem as bwa_mem_align { input: fastq=fastq, bwadb_tar_gz=reference_tar_gz, ncpu=n_threads, memory_gb=15 }
         }
     }
     if (aligner == "star") {
@@ -92,16 +93,24 @@ workflow xenocp {
         call xenocp_tools.cleanse { input: input_bam=pair.left, unmap_reads=pair.right, stringency=validation_stringency }
     }
 
-    call xenocp_tools.merge_markdup_index { input: input_bams=flatten([cleanse.cleaned_bam, [unmapped.unmapped_bam]]), output_bam=name, skip_dup=skip_duplicate_marking }
+    call xenocp_tools.merge_markdup_index as final_bam { input: input_bams=flatten([cleanse.cleaned_bam, [unmapped.unmapped_bam]]), output_bam=output_name, skip_dup=skip_duplicate_marking }
+
+    call xenocp_tools.qc { input: input_bam=final_bam.final_bam, input_bai=final_bam.final_bai, flagstat=final_bam.flagstat }
+
+    scatter(bam in create_contam_list.output_tie_bam){
+        call picard.sort as tie_sort { input: bam=bam, sort_order="coordinate" }
+    }
+
+    call xenocp_tools.merge_markdup_index as combine_tie_bam { input: input_bams=tie_sort.sorted_bam, output_bam=name+".tie.bam", skip_dup=true }
 
-    call xenocp_tools.qc { input: input_bam=merge_markdup_index.final_bam, input_bai=merge_markdup_index.final_bai, flagstat=merge_markdup_index.flagstat }
+    call xenocp_tools.combine_files { input: input_files=create_contam_list.contam_list, output_file=name+".contam.txt" }
 
     output {
-        File bam = merge_markdup_index.final_bam
-        File bam_index = merge_markdup_index.final_bai
-        File bam_md5 = merge_markdup_index.final_md5
-        File flagstat = merge_markdup_index.flagstat
-        Array[File] contam_list = create_contam_list.contam_list
-        Array[File] tie_bam = create_contam_list.output_tie_bam
+        File bam = final_bam.final_bam
+        File bam_index = final_bam.final_bai
+        File bam_md5 = final_bam.final_md5
+        File flagstat = final_bam.flagstat
+        File contam_list = combine_files.final_file
+        File tie_bam = combine_tie_bam.final_bam
     }
 }