diff --git a/.github/workflows/rsem1.2.21docker-publish.yml b/.github/workflows/rsem1.2.21docker-publish.yml
new file mode 100644
index 0000000..f876508
--- /dev/null
+++ b/.github/workflows/rsem1.2.21docker-publish.yml
@@ -0,0 +1,90 @@
+name: Docker
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+on:
+  #schedule:
+    #- cron: '37 6 * * *'
+  push:
+    branches: [ "master" ]
+    # Publish semver tags as releases.
+    #tags: [ 'v*.*.*' ]
+  pull_request:
+    branches: [ "master" ]
+
+env:
+  # Use docker.io for Docker Hub if empty
+  REGISTRY: ghcr.io
+  # github.repository as <account>/<repo>
+  IMAGE_NAME: ${{ github.repository }}/tools/rsem
+
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      # This is used to complete the identity challenge
+      # with sigstore/fulcio when running outside of PRs.
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      # Install the cosign tool except on PR
+      # https://github.com/sigstore/cosign-installer
+     # - name: Install cosign
+       # if: github.event_name != 'pull_request'
+     #  uses: sigstore/cosign-installer@d6a3abf1bdea83574e28d40543793018b6035605
+       # with:
+       #   cosign-release: 'v1.7.1'
+
+
+      # Workaround: https://github.com/docker/build-push-action/issues/461
+      - name: Setup Docker buildx
+        uses: docker/setup-buildx-action@79abd3f86f79a9d68a23c75a09a9a85889262adf
+
+      # Login against a Docker registry except on PR
+      # https://github.com/docker/login-action
+      
+     # - name: Log into registry Docker hub
+        #if: github.event_name != 'pull_request'
+       # uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+      #  with:
+       #   username: ${{ secrets.DOCKERHUB_USERNAME }}
+       #   password: ${{ secrets.DOCKERHUB_PASSWORD }}
+          
+      - name: Log in to the Container registry 
+        uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # Extract metadata (tags, labels) for Docker
+      # https://github.com/docker/metadata-action
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: 
+            ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+            #docker.io/reddylab/rsem
+          tags: latest
+
+      # Build and push Docker image with Buildx (don't push on PR)
+      # https://github.com/docker/build-push-action
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@ac9327eae2b366085ac7f6a2d02df8aa8ead720a
+        with:
+          context: ./tools/rsem/1.2.21/
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
diff --git a/.github/workflows/star-utils.yml b/.github/workflows/star-utils.yml
new file mode 100644
index 0000000..dd82456
--- /dev/null
+++ b/.github/workflows/star-utils.yml
@@ -0,0 +1,89 @@
+name: Docker
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation
+
+on:
+  #schedule:
+   # - cron: '43 13 * * *'
+  push:
+    branches: [ "master" ]
+    # Publish semver tags as releases.
+   # tags: [ v*.*.*]
+  pull_request:
+    branches: [ "master" ]
+
+env:
+  # Use docker.io for Docker Hub if empty
+ REGISTRY: ghcr.io
+    
+  # github.repository as <account>/<repo>
+ IMAGE_NAME: 
+      ${{ github.repository }}/tools/star-utils   
+
+jobs:
+  build:
+ 
+    name: Push Docker image to multiple registries
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      # This is used to complete the identity challenge
+      # with sigstore/fulcio when running outside of PRs.
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      # Install the cosign tool except on PR
+      # https://github.com/sigstore/cosign-installer
+      #- name: Install cosign
+        #if: github.event_name != 'pull_request'
+       # uses: sigstore/cosign-installer@d6a3abf1bdea83574e28d40543793018b6035605
+       # with:
+       #   cosign-release: 'v1.7.1'
+
+      # Workaround: https://github.com/docker/build-push-action/issues/461
+      - name: Setup Docker buildx
+        uses: docker/setup-buildx-action@79abd3f86f79a9d68a23c75a09a9a85889262adf
+
+      # Login against a Docker registry except on PR
+      # https://github.com/docker/login-action
+     # - name: Log into Docker hub 
+        #if: github.event_name != 'pull_request'
+        #uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+        #with:
+       #   username: ${{ secrets.DOCKER_USERNAME }}
+        #  password: ${{ secrets.DOCKER_TOKEN }}
+          
+      - name: Log in to the Container registry  
+        uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # Extract metadata (tags, labels) for Docker
+      # https://github.com/docker/metadata-action
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: |
+              ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}  
+          tags: latest    
+      # Build and push Docker image with Buildx (don't push on PR)
+      # https://github.com/docker/build-push-action
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@ac9327eae2b366085ac7f6a2d02df8aa8ead720a
+        with:
+          context: ./tools/star-utils/
+          #push: ${{ github.event_name != 'pull_request' }}
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
diff --git a/.github/workflows/windowtrimmer.yml b/.github/workflows/windowtrimmer.yml
new file mode 100644
index 0000000..af021da
--- /dev/null
+++ b/.github/workflows/windowtrimmer.yml
@@ -0,0 +1,101 @@
+name: Docker
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+on:
+  #schedule:
+   # - cron: '15 23 * * *'
+  push:
+    branches: [ "master" ]
+    # Publish semver tags as releases.
+    #tags: [ 'v*.*.*' ]
+  pull_request:
+    branches: [ "master" ]
+
+env:
+  # Use docker.io for Docker Hub if empty
+  REGISTRY: ghcr.io
+  # github.repository as <account>/<repo>
+  IMAGE_NAME: ${{ github.repository }}/tools/windowtrimmer
+
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      # This is used to complete the identity challenge
+      # with sigstore/fulcio when running outside of PRs.
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      # Install the cosign tool except on PR
+      # https://github.com/sigstore/cosign-installer
+      #- name: Install cosign
+       # if: github.event_name != 'pull_request'
+        #uses: sigstore/cosign-installer@d6a3abf1bdea83574e28d40543793018b6035605
+        #with:
+         # cosign-release: 'v1.7.1'
+
+
+      # Workaround: https://github.com/docker/build-push-action/issues/461
+      - name: Setup Docker buildx
+        uses: docker/setup-buildx-action@79abd3f86f79a9d68a23c75a09a9a85889262adf
+
+      # Login against a Docker registry except on PR
+      # https://github.com/docker/login-action
+      # - name: Log into Docker hub 
+        #if: github.event_name != 'pull_request'
+        #uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+        #with:
+       #   username: ${{ secrets.DOCKER_USERNAME }}
+        #  password: ${{ secrets.DOCKER_TOKEN }}
+          
+      - name: Log in to the Container registry  
+        #if: github.event_name != 'pull_request'
+        uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # Extract metadata (tags, labels) for Docker
+      # https://github.com/docker/metadata-action
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: latest
+
+      # Build and push Docker image with Buildx (don't push on PR)
+      # https://github.com/docker/build-push-action
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@ac9327eae2b366085ac7f6a2d02df8aa8ead720a
+        with:
+          context: ./tools/windowtrimmer/
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+      # Sign the resulting Docker image digest except on PRs.
+      # This will only write to the public Rekor transparency log when the Docker
+      # repository is public to avoid leaking data.  If you would like to publish
+      # transparency data even for private images, pass --force to cosign below.
+      # https://github.com/sigstore/cosign
+      #- name: Sign the published Docker image
+      #  if: ${{ github.event_name != 'pull_request' }}
+      #  env:
+      #    COSIGN_EXPERIMENTAL: "true"
+        # This step uses the identity token to provision an ephemeral certificate
+        # against the sigstore community Fulcio instance.
+      #  run: cosign sign ${{ steps.meta.outputs.tags }}@${{ steps.build-and-push.outputs.digest }}
diff --git a/tools/rsem/1.2.21/Dockerfile b/tools/rsem/1.2.21/Dockerfile
new file mode 100644
index 0000000..0be32e3
--- /dev/null
+++ b/tools/rsem/1.2.21/Dockerfile
@@ -0,0 +1,48 @@
+FROM phusion/baseimage:focal-1.2.0
+MAINTAINER Alejandro Barrera <alejandro.barrera@duke.edu>
+
+# Install dependencies
+RUN apt-get update && apt-get install -y \
+  build-essential \
+  g++ \
+  zlib1g-dev \
+  libncurses-dev \
+  curl \
+  unzip
+
+#########################################################
+# NOTE: Added here Bowtie image given that CWL          #
+# ^^^^  will not allow multiple Docker dependencies     #
+#       at this point.                                  #
+#########################################################
+# Installs bowtie from compiled distribution into /opt/bowtie
+ENV BOWTIE_URL=http://sourceforge.net/projects/bowtie-bio/files/bowtie
+ENV BOWTIE_RELEASE=0.12.9
+ENV DEST_DIR=/opt
+
+# Download Bowtie, unzip it and remove .zip file
+RUN curl -SLo ${DEST_DIR}/bowtie-${BOWTIE_RELEASE}.zip ${BOWTIE_URL}/${BOWTIE_RELEASE}/bowtie-${BOWTIE_RELEASE}-linux-x86_64.zip/download && unzip ${DEST_DIR}/bowtie-${BOWTIE_RELEASE}.zip -d ${DEST_DIR} && rm ${DEST_DIR}/bowtie-${BOWTIE_RELEASE}.zip
+
+# Add bowtie path to the enviroment
+ENV PATH=${DEST_DIR}/bowtie-${BOWTIE_RELEASE}:$PATH
+
+# Define ENV variables for download
+ENV RSEM_RELEASE=1.2.21
+ENV RSEM_URL=https://github.com/deweylab/RSEM/archive/refs/tags/v${RSEM_RELEASE}.tar.gz
+#ENV RSEM_URL=https://github.com/deweylab/RSEM/releases/tag/v${RSEM_RELEASE}.tar.gz
+ENV DEST_DIR=/opt
+
+# Download and unpack RSEM sources, make & install and remove unnecessary files
+RUN curl -SLo ${DEST_DIR}/RSEM-${RSEM_RELEASE}.tar.gz ${RSEM_URL} && \
+    tar xzvf ${DEST_DIR}/RSEM-${RSEM_RELEASE}.tar.gz -C ${DEST_DIR} && \
+    cd ${DEST_DIR}/RSEM-${RSEM_RELEASE} && \
+    sed -i.bak "s/CC = g++/CC = g++ -std=gnu++98/" Makefile && \
+    make && \
+    rm -rf ${DEST_DIR}/RSEM-${RSEM_RELEASE}.tar.gz
+
+# Add RSEM path to ENV path
+ENV PATH=${DEST_DIR}/RSEM-${RSEM_RELEASE}/:$PATH
+
+# List executables provided by rsem
+
+CMD ["find", "/opt/", "-executable", "-type", "f", "-iname", "rsem*"]
diff --git a/tools/star-utils/Dockerfile b/tools/star-utils/Dockerfile
new file mode 100644
index 0000000..bd66c6e
--- /dev/null
+++ b/tools/star-utils/Dockerfile
@@ -0,0 +1,11 @@
+FROM python:2.7
+MAINTAINER alejandro.barrera@duke.edu
+
+ADD src /src
+WORKDIR /src
+
+RUN pip install -r /src/requirements.txt
+
+RUN chmod +x /src/create_SJ.out.tab.Pass1.conservative.sjdb.py
+ENV PATH /src/:$PATH
+CMD ["create_SJ.out.tab.Pass1.conservative.sjdb.py"]
diff --git a/tools/star-utils/src/create_SJ.out.tab.Pass1.conservative.sjdb.py b/tools/star-utils/src/create_SJ.out.tab.Pass1.conservative.sjdb.py
new file mode 100644
index 0000000..747d0eb
--- /dev/null
+++ b/tools/star-utils/src/create_SJ.out.tab.Pass1.conservative.sjdb.py
@@ -0,0 +1,62 @@
+#!/usr/bin/env python
+##################################################
+#  create_SJ.out.tab.Pass1.conservative.sjdb.py
+#
+#  Merge the STAR 1-pass novel splice junction databases ('SJ.out.tab').
+#  Save only those splice junctions in autosomes and sex chromosomes.  
+#  Filter out splice junctions that are non-canonical,
+#  supported by only 10 or fewer reads.
+#
+##################################################
+import pandas as pd
+from collections import defaultdict
+from sys import argv
+
+SJ_DBs = argv[1].split(',')
+SJ_DB_out = argv[2]
+
+# samples = [s.replace(base, '').replace(suffix, '') for s in SJ_DBs]
+
+# canonical_chroms = set(['chr'+str(x) for x in range(1,24)])
+# canonical_chroms.add('chrX')
+# canonical_chroms.add('chrY')
+
+strand_dict = {}
+strand_dict[0],strand_dict[1],strand_dict[2] = '.','+','-'
+
+# SJ.out.tab format:
+    
+# Column 1: chromosome
+# Column 2: first base of the intron (1-based)
+# Column 3: last base of the intron (1-based)
+# Column 4: strand
+# Column 5: intron motif: 0: non-canonical; 1: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT
+# Column 6: reserved
+# Column 7: number of uniquely mapping reads crossing the junction
+# Column 8: reserved
+# Column 9: maximum left/right overhang 
+
+splice_dict = defaultdict(dict)
+for i,  SJ_DB in enumerate(SJ_DBs):
+    columns = ['chrom','start','end','strand','intron_motif','reserved','num_uniq_mapped_reads','reserved','left/right_overhang']
+    SJ_DB = pd.read_csv(SJ_DB, delim_whitespace=True, header=None, names = columns)
+    # filter out non-canonical splice juntions
+    SJ_DB = SJ_DB[SJ_DB.intron_motif != 0]
+    # filter out splice junctions without support of greater than 1 unique read
+    SJ_DB = SJ_DB[SJ_DB.num_uniq_mapped_reads > 1]
+    SJ_DB['strand'] = [strand_dict[strand] for strand in SJ_DB['strand']]
+    for chrom, start, end, strand in zip(SJ_DB.chrom, SJ_DB.start, SJ_DB.end, SJ_DB.strand):
+        if (chrom,start,end,strand) in splice_dict:
+            splice_dict[(chrom,start,end,strand)] += 1
+        else:
+            splice_dict[(chrom,start,end,strand)] = 1
+
+splice_sites = splice_dict.keys()
+splice_sites = sorted(splice_sites, key=lambda s: int(s[1]))
+splice_sites = sorted(splice_sites, key=lambda s: s[0][3:])
+# splice_sites = [splice_site for splice_site in splice_sites if splice_site[0] in canonical_chroms]
+
+splice_sites = ['\t'.join([str(x) for x in splice_site]) for splice_site in splice_sites]
+out = open(SJ_DB_out,'w')
+out.write('\n'.join(splice_sites) + '\n')
+out.close()
diff --git a/tools/star-utils/src/requirements.txt b/tools/star-utils/src/requirements.txt
new file mode 100644
index 0000000..b06e5c2
--- /dev/null
+++ b/tools/star-utils/src/requirements.txt
@@ -0,0 +1 @@
+pandas==0.16.2
diff --git a/tools/windowtrimmer/Dockerfile b/tools/windowtrimmer/Dockerfile
new file mode 100644
index 0000000..f8ec77e
--- /dev/null
+++ b/tools/windowtrimmer/Dockerfile
@@ -0,0 +1,10 @@
+FROM python:2.7
+MAINTAINER alejandro.barrera@duke.edu
+
+ADD src /src
+WORKDIR /src
+
+RUN chmod +x /src/windowTrimmer.py
+ENV PATH /src/:$PATH
+
+CMD ["windowTrimmer.py"]
diff --git a/tools/windowtrimmer/src/windowTrimmer.py b/tools/windowtrimmer/src/windowTrimmer.py
new file mode 100644
index 0000000..1b1c157
--- /dev/null
+++ b/tools/windowtrimmer/src/windowTrimmer.py
@@ -0,0 +1,131 @@
+#!/usr/bin/env python2.7
+
+# Written by Thomas Konneker, adapted by Ian McDowell and Alejandro Barrera
+# This script is intended to crawl through bed files to filter
+# out reads that are too concentrated within a specified base-pair
+# window.  This is presumably because they are PCR artifacts.
+# See Boyle et. al 2011, Genome Research
+# Currently this program does not 'window' in the traditional sense
+# of tiling out the genome and then evaluating those
+# windows. Instead starts a window at the next place there is an entry
+# that follows the previous window.
+
+# Modified 7-1-2014 to include requirement for 2 reads minimum for removal of putative artifact.
+# Modified 4-25-2016 to reformat code including option to specify a BED file instead of reading stdin.
+
+import sys
+from optparse import OptionParser
+from collections import Counter
+
+
+class BedEntry:
+    def __init__(self, chromosome, start, end, name,
+                 score, strand, fullBedLine):
+        self.chromosome = str(chromosome)
+        self.startposition = int(start)
+        self.endposition = int(end)
+        self.name = name
+        self.score = score
+        self.strand = strand
+        self.fullBedLine = fullBedLine
+
+
+class BedReader:
+    """BED file reader object. For parsing and yielding bed entries from a file."""
+
+    def __init__(self, inFile):
+        self.inFile = inFile
+
+    def spitLines(self):
+        for line in self.inFile:
+            fullBedLine = line.strip('\n\r')
+            wholeline = fullBedLine.split('\t')
+            bedLine = BedEntry(wholeline[0], wholeline[1], wholeline[2],
+                               wholeline[3], wholeline[4], wholeline[5], fullBedLine)
+            yield bedLine
+
+
+def windowChooser(position_list, cutoff):
+    """Evaluate whether a list of bed is too concentrated at a single position, given a concentration threshold.
+    Returns: boolean.
+    """
+    position_list, cutoff = position_list, cutoff
+    if position_list:
+        count = Counter(position_list)
+        peak = float(count.most_common()[0][1])
+        if peak / len(position_list) >= cutoff and peak >= 2:
+            return 0
+        else:
+            return 1
+    else:
+        return 1
+
+
+def windowizer(bedIn, windowsize, cutoff):
+    """Compute bedlines that fall under the cutoff criteria for concentration of reads to a single base pair within a window."""
+
+    windowend = 0
+    current_chr = "chr1"
+    full_bed_list = []
+    position_list = []
+    for line in bedIn.spitLines():
+        if line.startposition > windowend:
+            windowstart = line.startposition
+            windowend = windowstart + windowsize
+            if windowChooser(position_list, cutoff):
+                for item in full_bed_list:
+                    print item
+            position_list = [line.startposition]
+            full_bed_list = [line.fullBedLine]
+        elif line.startposition <= windowend:
+            if line.chromosome == current_chr:
+                position_list.append(line.startposition)
+                full_bed_list.append(line.fullBedLine)
+            else:
+                current_chr = line.chromosome
+                windowstart = line.startposition
+                windowend = windowstart + windowsize
+                if windowChooser(position_list, cutoff):
+                    for item in full_bed_list:
+                        print item
+                position_list = [line.startposition]
+                full_bed_list = [line.fullBedLine]
+        else:
+            if windowChooser(position_list, cutoff):
+                for item in full_bed_list:
+                    print item
+
+
+def main():
+    parser = OptionParser()
+    parser.add_option('-w', '--windowsize', type='int',
+                      dest='windowsize', default=31,
+                      help='threshold for trimming reads that have \
+              the same mapping start position')
+    parser.add_option('-c', '--cutoff', type="float",
+                      dest='cutoff', default=0.70,
+                      help="threshold for concentration at a single base \
+              within a window to cutoff")
+    parser.add_option('-i', '--infile', type="str", dest='infile',
+                      help="Input BED file to be scanned and filtered")
+
+    (options, args) = parser.parse_args()
+
+    windowsize = options.windowsize
+    cutoff = options.cutoff
+    infile_name = options.infile
+
+    # parse command line
+    if infile_name:
+        infile = open(infile_name)
+    else:
+        infile = sys.stdin
+    entry = BedReader(infile)
+    windowizer(entry, windowsize, cutoff)
+
+    if infile_name is not sys.stdin:
+        infile.close()
+
+
+if __name__ == '__main__':
+    main()