diff --git a/utils/docking/diffdock/diffdock-tool/.bumpversion.cfg b/utils/docking/diffdock/diffdock-tool/.bumpversion.cfg
new file mode 100644
index 00000000..80ed4022
--- /dev/null
+++ b/utils/docking/diffdock/diffdock-tool/.bumpversion.cfg
@@ -0,0 +1,29 @@
+[bumpversion]
+current_version = 0.1.0
+commit = False
+tag = False
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
+serialize = 
+	{major}.{minor}.{patch}-{release}{dev}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = _
+first_value = dev
+values = 
+	dev
+	_
+
+[bumpversion:part:dev]
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:VERSION]
+
+[bumpversion:file:README.md]
+
+[bumpversion:file:plugin.json]
+
+[bumpversion:file:src/polus/mm/utils/diffdock/__init__.py]
diff --git a/utils/docking/diffdock/diffdock-tool/.dockerignore b/utils/docking/diffdock/diffdock-tool/.dockerignore
new file mode 100644
index 00000000..7c603f81
--- /dev/null
+++ b/utils/docking/diffdock/diffdock-tool/.dockerignore
@@ -0,0 +1,4 @@
+.venv
+out
+tests
+__pycache__
diff --git a/utils/docking/diffdock/diffdock-tool/.gitattributes b/utils/docking/diffdock/diffdock-tool/.gitattributes
new file mode 100644
index 00000000..07fedc1e
--- /dev/null
+++ b/utils/docking/diffdock/diffdock-tool/.gitattributes
@@ -0,0 +1,5 @@
+*.pdb filter=lfs diff=lfs merge=lfs -text
+*.pdbqt filter=lfs diff=lfs merge=lfs -text
+*.mol2 filter=lfs diff=lfs merge=lfs -text
+*.xlsx filter=lfs diff=lfs merge=lfs -text
+*.sdf filter=lfs diff=lfs merge=lfs -text
diff --git a/utils/docking/diffdock/diffdock-tool/.gitignore b/utils/docking/diffdock/diffdock-tool/.gitignore
new file mode 100644
index 00000000..c04bc49f
--- /dev/null
+++ b/utils/docking/diffdock/diffdock-tool/.gitignore
@@ -0,0 +1 @@
+poetry.lock
diff --git a/utils/docking/diffdock/diffdock-tool/CHANGELOG.md b/utils/docking/diffdock/diffdock-tool/CHANGELOG.md
new file mode 100644
index 00000000..b67793f7
--- /dev/null
+++ b/utils/docking/diffdock/diffdock-tool/CHANGELOG.md
@@ -0,0 +1,5 @@
+# CHANGELOG
+
+## 0.1.0
+
+Initial release.
diff --git a/utils/docking/diffdock/diffdock-tool/Dockerfile_diffdock_gpu b/utils/docking/diffdock/diffdock-tool/Dockerfile_diffdock_gpu
new file mode 100644
index 00000000..9d873d27
--- /dev/null
+++ b/utils/docking/diffdock/diffdock-tool/Dockerfile_diffdock_gpu
@@ -0,0 +1,58 @@
+# docker build -f Dockerfile_diffdock_gpu -t mrbrandonwalker/diffdock_gpu .
+
+FROM nvidia/cuda:11.7.1-cudnn8-devel-ubuntu20.04 as devel
+
+# Install conda / mamba
+RUN apt-get update && apt-get install -y wget git build-essential
+
+RUN CONDA="Mambaforge-Linux-x86_64.sh" && \
+    wget --quiet https://github.com/conda-forge/miniforge/releases/latest/download/$CONDA && \
+    chmod +x $CONDA && \
+    ./$CONDA -b -p /mambaforge && \
+    rm -f $CONDA
+ENV PATH /mambaforge/bin:$PATH
+
+RUN conda install pytorch==1.13.0 pytorch-cuda=11.7 pytorch-cluster -c pytorch -c nvidia -c pyg
+
+# Website suggests torch 1.12 but only 1.12 doesn't exist with cuda 11.7 https://github.com/gcorso/DiffDock https://data.pyg.org/whl/torch-1.13.0+cu117.html
+# Need to install pytorch first before other torch packages
+# Cannot use conda for these packages otherwise will install them with a default CUDA (not same as cuda 11.7)
+# so need to specify which package versions (CUDA and Torch)
+# If install pytorch-cluster below with rest of torch packages, the will get error Not compiled with CUDA support
+
+RUN pip install torch-scatter torch-sparse torch-spline-conv torch-geometric==2.0.4 -f https://data.pyg.org/whl/torch-1.13.0+cu117.html
+
+RUN conda install PyYAML scipy "networkx[default]" biopython rdkit e3nn spyrmsd pandas biopandas
+
+# See install for GPU https://github.com/gcorso/DiffDock, some packages are only in pip
+
+RUN pip install 'openfold @ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307' 'dllogger @ git+https://github.com/NVIDIA/dllogger.git' "fair-esm[esmfold]"
+
+RUN git clone https://github.com/gcorso/DiffDock.git
+
+WORKDIR /DiffDock
+
+RUN conda init bash
+
+# generate the pre-computed cached files for speeding up the inference
+# See https://github.com/gcorso/DiffDock#running-diffdock-on-your-own-complexes
+# Note that the first time you run DiffDock on a device the program will precompute and store in cache look-up tables for SO(2) and SO(3) distributions (typically takes a couple of minutes), this won't be repeated in following runs.
+# output pre-computed cached files are of the format .*.npy such as .so3_omegas_array2.npy, .so3_cdf_vals2.npy, .so3_score_norms2.npy, .so3_exp_score_norms2.npy
+RUN python -m inference --protein_ligand_csv data/protein_ligand_example_csv.csv --out_dir results/user_predictions_small --inference_steps 1 --samples_per_complex 1 --batch_size 1 --actual_steps 1
+
+# Delete output results so not in same output folder as future runs
+RUN rm -r results/user_predictions_small
+
+# Clean up temp files
+RUN mamba clean --all --yes
+
+# Now copy everything into a minimal cuda runtime base image.
+FROM nvidia/cuda:11.7.1-cudnn8-runtime-ubuntu20.04 as runtime
+
+COPY --from=devel DiffDock/ DiffDock/
+COPY --from=devel mambaforge/ mambaforge/
+
+# shell file to copy cached files, run diffdock and remove large cached files after execution
+ADD diffdock_cmds.sh /DiffDock/
+
+ENV PATH /mambaforge/bin:$PATH
diff --git a/utils/docking/diffdock/diffdock-tool/README.md b/utils/docking/diffdock/diffdock-tool/README.md
new file mode 100644
index 00000000..0658c289
--- /dev/null
+++ b/utils/docking/diffdock/diffdock-tool/README.md
@@ -0,0 +1,22 @@
+# diffdock (0.1.0)
+
+DiffDock Diffusion based protein ligand docking
+
+## Options
+
+This plugin takes     11     input arguments and 4 output argument:
+
+| Name          | Description             | I/O    | Type   | Default |
+|---------------|-------------------------|--------|--------|---------|
+| protein_path | Protein input file | Input | File | File |
+| ligand_path | Ligand input file | Input | File | File |
+| inference_steps | Number of inference steps for diffusion | Input | int | int |
+| samples_per_complex | Number of pose samples to generate per complex | Input | int | int |
+| batch_size | Batch size | Input | int | int |
+| out_dir | Output directory to save poses | Input | string | string |
+| model_dir | Input model directory to use | Input | string | string |
+| confidence_model_dir | Input confidence model directory | Input | string | string |
+| complex_name | Name of complex | Input | string | string |
+| max_confident_pose | Highest confident pose | Output | File | File |
+| output_files | The output poses | Output | File[] | File[] |
+| execution_time | Time to run DiffDock | Output | float | float |
diff --git a/utils/docking/diffdock/diffdock-tool/VERSION b/utils/docking/diffdock/diffdock-tool/VERSION
new file mode 100644
index 00000000..6e8bf73a
--- /dev/null
+++ b/utils/docking/diffdock/diffdock-tool/VERSION
@@ -0,0 +1 @@
+0.1.0
diff --git a/utils/docking/diffdock/diffdock-tool/diffdock.cwl b/utils/docking/diffdock/diffdock-tool/diffdock.cwl
new file mode 100644
index 00000000..e83d1ce6
--- /dev/null
+++ b/utils/docking/diffdock/diffdock-tool/diffdock.cwl
@@ -0,0 +1,138 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: DiffDock Diffusion based protein ligand docking
+
+doc: |-
+  DiffDock Diffusion based protein ligand docking
+
+baseCommand: ["bash", "/DiffDock/diffdock_cmds.sh"]
+
+hints:
+  cwltool:CUDARequirement:
+    cudaVersionMin: "11.7"
+    cudaComputeCapability: "3.0"
+    cudaDeviceCountMin: 1
+    cudaDeviceCountMax: 1
+  DockerRequirement:
+    dockerPull: mrbrandonwalker/diffdock_gpu
+
+requirements:
+  InlineJavascriptRequirement: {}
+inputs:
+
+  protein_path:
+    type: File
+    format: edam:format_1476
+    inputBinding:
+      prefix: --protein_path
+
+  ligand_path:
+    type: File
+    format: edam:format_3814
+    inputBinding:
+      prefix: --ligand_description
+
+  inference_steps:
+    label: number of reverse diffusion steps
+    type: int?
+    inputBinding:
+      prefix: --inference_steps
+    default: 20
+
+  samples_per_complex:
+    label: Number of sample poses to generate per complex
+    type: int?
+    inputBinding:
+      prefix: --samples_per_complex
+    default: 40
+
+  batch_size:
+    label: input batch size for neural net
+    type: int?
+    inputBinding:
+      prefix: --batch_size
+    default: 1
+
+  out_dir:
+    label: where output from diffdock is saved
+    type: string?
+    inputBinding:
+      prefix: --out_dir
+    default: results/
+
+  model_dir:
+    label: directory of DiffDock score model from paper
+    type: string?
+    inputBinding:
+      prefix: --model_dir
+    default:  /DiffDock/workdir/paper_score_model/
+
+  confidence_model_dir:
+    label: directory of DiffDock confidence model from paper
+    type: string?
+    inputBinding:
+      prefix: --confidence_model_dir
+    default:  /DiffDock/workdir/paper_confidence_model
+
+  complex_name:
+    label: name of folder with pose outputs that will be saved under out_dir folder
+    type: string?
+    inputBinding:
+      prefix: --complex_name
+    default:  outputs
+
+  output_files:
+    type: string?
+
+  max_confident_pose:
+    type: string?
+
+outputs:
+
+  max_confident_pose:
+    type: File
+    outputBinding:
+      # the diffdock developers copy only the top ranked pose to a new file rank1.sdf
+      glob: $(inputs.out_dir)/$(inputs.complex_name)/rank1.sdf
+    format: edam:format_3814
+
+  output_files:
+    type: File[]
+    outputBinding:
+      # all other output files besides rank1.sdf have confidence information in them rank*_confidence*.sdf
+      glob: $(inputs.out_dir)/$(inputs.complex_name)/rank*_confidence*.sdf
+    format: edam:format_3814
+
+  stderr:
+    type: File
+    outputBinding:
+      glob: stderr
+
+  execution_time:
+    label: Time to run DiffDock
+    doc: |-
+      Time to run DiffDock
+    type: float
+    outputBinding:
+      glob: stderr
+      loadContents: true
+      outputEval: |
+        ${
+          // the time command outputs to stderr and not to stdout
+          // example output below, parse the float value of seconds (first item in line)
+          // 1it [00:41, 41.03s/it]
+          // 78.909
+          return self[0].contents.split("\n").map(str => parseFloat(str)).reverse().find(num => !isNaN(num));
+        }
+
+stderr: stderr
+
+$namespaces:
+  edam: https://edamontology.org/
+  cwltool: http://commonwl.org/cwltool#
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl
diff --git a/utils/docking/diffdock/diffdock-tool/diffdock_cmds.sh b/utils/docking/diffdock/diffdock-tool/diffdock_cmds.sh
new file mode 100644
index 00000000..a2c3b4ce
--- /dev/null
+++ b/utils/docking/diffdock/diffdock-tool/diffdock_cmds.sh
@@ -0,0 +1,7 @@
+#!/bin/bash -e
+# copy cached files to current directory
+cp /DiffDock/.*.npy .
+TIMEFORMAT=%R && time python /DiffDock/inference.py "$@"
+# need to remove large files otherwise cachedir folder will be 3GB each!!
+rm .*.npy
+rm -r .cache/
diff --git a/utils/docking/diffdock/diffdock-tool/ict.yml b/utils/docking/diffdock/diffdock-tool/ict.yml
new file mode 100644
index 00000000..d2371fba
--- /dev/null
+++ b/utils/docking/diffdock/diffdock-tool/ict.yml
@@ -0,0 +1,135 @@
+specVersion: "0.1.0"
+name: diffdock
+version: 0.1.0
+container: diffdock-tool
+entrypoint:
+title: diffdock
+description: DiffDock Diffusion based protein ligand docking
+author: Brandon Walker
+contact: brandon.walker@axleinfo.com
+repository:
+documentation:
+citation:
+
+inputs:
+  - name: protein_path
+    required: true
+    description:
+    type: File
+    format:
+      uri: edam:format_1476
+  - name: ligand_path
+    required: true
+    description:
+    type: File
+    format:
+      uri: edam:format_3814
+  - name: inference_steps
+    required: true
+    description:
+    type: int
+    defaultValue: 20
+  - name: samples_per_complex
+    required: true
+    description:
+    type: int
+    defaultValue: 40
+  - name: batch_size
+    required: true
+    description:
+    type: int
+    defaultValue: 1
+  - name: out_dir
+    required: true
+    description:
+    type: string
+    defaultValue: results/
+  - name: model_dir
+    required: true
+    description:
+    type: string
+    defaultValue: /DiffDock/workdir/paper_score_model/
+  - name: confidence_model_dir
+    required: true
+    description:
+    type: string
+    defaultValue: /DiffDock/workdir/paper_confidence_model
+  - name: complex_name
+    required: true
+    description:
+    type: string
+    defaultValue: outputs
+  - name: output_files
+    required: true
+    description:
+    type: string
+  - name: max_confident_pose
+    required: true
+    description:
+    type: string
+outputs:
+  - name: max_confident_pose
+    required: true
+    description:
+    type: File
+    format:
+      uri: edam:format_3814
+  - name: output_files
+    required: true
+    description:
+    type: File[]
+    format:
+      uri: edam:format_3814
+  - name: stderr
+    required: true
+    description:
+    type: File
+  - name: execution_time
+    required: true
+    description: Time to run DiffDock
+    type: float
+ui:
+  - key: inputs.protein_path
+    title: "protein_path: "
+    description: ""
+    type: File
+  - key: inputs.ligand_path
+    title: "ligand_path: "
+    description: ""
+    type: File
+  - key: inputs.inference_steps
+    title: "inference_steps: "
+    description: ""
+    type: int
+  - key: inputs.samples_per_complex
+    title: "samples_per_complex: "
+    description: ""
+    type: int
+  - key: inputs.batch_size
+    title: "batch_size: "
+    description: ""
+    type: int
+  - key: inputs.out_dir
+    title: "out_dir: "
+    description: ""
+    type: string
+  - key: inputs.model_dir
+    title: "model_dir: "
+    description: ""
+    type: string
+  - key: inputs.confidence_model_dir
+    title: "confidence_model_dir: "
+    description: ""
+    type: string
+  - key: inputs.complex_name
+    title: "complex_name: "
+    description: ""
+    type: string
+  - key: inputs.output_files
+    title: "output_files: "
+    description: ""
+    type: string
+  - key: inputs.max_confident_pose
+    title: "max_confident_pose: "
+    description: ""
+    type: string
diff --git a/utils/docking/diffdock/diffdock-tool/pyproject.toml b/utils/docking/diffdock/diffdock-tool/pyproject.toml
new file mode 100644
index 00000000..7609b230
--- /dev/null
+++ b/utils/docking/diffdock/diffdock-tool/pyproject.toml
@@ -0,0 +1,30 @@
+[tool.poetry]
+name = "polus-mm-utils-diffdock"
+version = "0.1.0"
+description = "DiffDock Diffusion based protein ligand docking"
+authors = ["Data Scientist <data.scientist@labshare.org>"]
+readme = "README.md"
+package-mode = false
+
+[tool.poetry.dependencies]
+python = ">=3.9,<3.12"
+cwl-utils = "0.33"
+cwltool = "3.1.20240404144621"
+
+[tool.poetry.group.dev.dependencies]
+bump2version = "^1.0.1"
+pytest = "^7.4"
+pytest-sugar = "^0.9.6"
+pre-commit = "^3.2.1"
+black = "^23.3.0"
+mypy = "^1.1.1"
+ruff = "^0.0.270"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.pytest.ini_options]
+pythonpath = [
+  "."
+]
diff --git a/utils/docking/diffdock/diffdock-tool/tests/5umx_ligand.sdf b/utils/docking/diffdock/diffdock-tool/tests/5umx_ligand.sdf
new file mode 100644
index 00000000..a4faf09d
--- /dev/null
+++ b/utils/docking/diffdock/diffdock-tool/tests/5umx_ligand.sdf
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b6c5502c25f2b4d271d1a00812373c094097470cdb8451170f30aa24122a94ad
+size 3315
diff --git a/utils/docking/diffdock/diffdock-tool/tests/5umx_protein.pdb b/utils/docking/diffdock/diffdock-tool/tests/5umx_protein.pdb
new file mode 100644
index 00000000..0c753aa6
--- /dev/null
+++ b/utils/docking/diffdock/diffdock-tool/tests/5umx_protein.pdb
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3121f590648faea13099e3053900626faf8e7b891f4214af35a557b125f11196
+size 197779
diff --git a/utils/docking/diffdock/diffdock-tool/tests/__init__.py b/utils/docking/diffdock/diffdock-tool/tests/__init__.py
new file mode 100644
index 00000000..d93c7a1e
--- /dev/null
+++ b/utils/docking/diffdock/diffdock-tool/tests/__init__.py
@@ -0,0 +1 @@
+"""Tests for diffdock."""
diff --git a/utils/docking/diffdock/diffdock-tool/tests/test_diffdock.py b/utils/docking/diffdock/diffdock-tool/tests/test_diffdock.py
new file mode 100644
index 00000000..5bd51f7d
--- /dev/null
+++ b/utils/docking/diffdock/diffdock-tool/tests/test_diffdock.py
@@ -0,0 +1,30 @@
+"""Tests for diffdock."""
+import sys
+from pathlib import Path
+
+current_dir = Path(__file__).resolve().parent
+target_dir = current_dir.parent.parent.parent / "cwl_utils"
+sys.path.append(str(target_dir))
+
+from cwl_utilities import call_cwltool  # noqa: E402
+from cwl_utilities import create_input_yaml  # noqa: E402
+from cwl_utilities import parse_cwl_arguments  # noqa: E402
+
+
+def test_diffdock() -> None:
+    """Test diffdock."""
+    cwl_file_str = "diffdock.cwl"
+    cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str)
+    input_to_props = parse_cwl_arguments(cwl_file)
+    file_path_str = "5umx_protein.pdb"
+    file_path = str(Path(__file__).resolve().parent / Path(file_path_str))
+    input_to_props["protein_path"]["path"] = file_path
+    file_path_str = "5umx_ligand.sdf"
+    file_path = str(Path(__file__).resolve().parent / Path(file_path_str))
+    input_to_props["ligand_path"]["path"] = file_path
+
+    input_yaml_path = Path("diffdock.yml")
+    create_input_yaml(input_to_props, input_yaml_path)
+
+    stdout, stderr = call_cwltool(cwl_file, input_yaml_path)
+    assert Path("rank1.sdf").exists()