diff --git a/config.py b/config.py
index e6ff35f..6840a7f 100644
--- a/config.py
+++ b/config.py
@@ -4,14 +4,15 @@
 LOG_GROUP_NAME = APP_NAME
 
 # DOCKER REGISTRY INFORMATION:
-DOCKERHUB_TAG = 'cellprofiler/distributed-cellprofiler:2.0.0_4.1.3'
+DOCKERHUB_TAG = 'cellprofiler/distributed-cellprofiler:2.0.0_4.2.4'
 
 # AWS GENERAL SETTINGS:
 AWS_REGION = 'us-east-1'
 AWS_PROFILE = 'default'                 # The same profile used by your AWS CLI installation
 SSH_KEY_NAME = 'your-key-file.pem'      # Expected to be in ~/.ssh
 AWS_BUCKET = 'your-bucket-name'         # Bucket to use for logging
-SOURCE_BUCKET = 'bucket-name'           # Bucket to download files from
+SOURCE_BUCKET = 'bucket-name'           # Bucket to download image files from
+WORKSPACE_BUCKET = 'bucket-name'        # Bucket to download non-image files from
 DESTINATION_BUCKET = 'bucket-name'      # Bucket to upload files to
 UPLOAD_FLAGS = ''                       # Any flags needed for upload to destination bucket
 
@@ -19,8 +20,8 @@
 ECS_CLUSTER = 'default'
 CLUSTER_MACHINES = 3
 TASKS_PER_MACHINE = 1
-MACHINE_TYPE = ['m4.xlarge']
-MACHINE_PRICE = 0.10
+MACHINE_TYPE = ['m5.xlarge']
+MACHINE_PRICE = 0.20
 EBS_VOL_SIZE = 30                       # In GB.  Minimum allowed is 22.
 DOWNLOAD_FILES = 'False'
 
diff --git a/documentation/DCP-documentation/step_1_configuration.md b/documentation/DCP-documentation/step_1_configuration.md
index 6e54969..272cbe7 100644
--- a/documentation/DCP-documentation/step_1_configuration.md
+++ b/documentation/DCP-documentation/step_1_configuration.md
@@ -25,7 +25,9 @@ For more information and examples, see [External Buckets](external_buckets.md).
 
 * **AWS_BUCKET:** The bucket to which you would like to write log files.
 This is generally the bucket in the account in which you are running compute.
-* **SOURCE_BUCKET:** The bucket where the files you will be reading are.
+* **SOURCE_BUCKET:** The bucket where the image files you will be reading are.
+Often, this is the same as AWS_BUCKET.
+* **WORKSPACE:** The bucket where non-image files you will be reading are (e.g. pipeline, load_data.csv, etc.).
 Often, this is the same as AWS_BUCKET.
 * **DESTINATION_BUCKET:** The bucket where you want to write your output files.
 Often, this is the same as AWS_BUCKET.
diff --git a/example_project/README.md b/example_project/README.md
index 3d064d1..25fdaef 100644
--- a/example_project/README.md
+++ b/example_project/README.md
@@ -1,3 +1,5 @@
+# Distributed-CellProfiler Minimal Example
+
 Included in this folder is all of the resources for running a complete mini-example of Distributed-Cellprofiler.
 It includes 3 sample image sets and a CellProfiler pipeline that identifies cells within the images and makes measuremements.
 It also includes the Distributed-CellProfiler files pre-configured to create a queue of all 3 jobs and spin up a spot fleet of 3 instances, each of which will process a single image set.
@@ -9,21 +11,23 @@ It also includes the Distributed-CellProfiler files pre-configured to create a q
 Before running this mini-example, you will need to set up your AWS infrastructure as described in our [online documentation](https://distributedscience.github.io/Distributed-CellProfiler/step_0_prep.html).
 This includes creating the fleet file that you will use in Step 3.
 
-Upload the 'sample_project' folder to the top level of your bucket. 
+Upload the 'sample_project' folder to the top level of your bucket.
 While in the `Distributed-CellProfiler` folder, use the following command, replacing `yourbucket` with your bucket name:
 
 ```bash
 # Copy example files to S3
 BUCKET=yourbucket
-aws s3 sync example_project/project_folder s3://${BUCKET}/project_folder
+aws s3 sync example_project/demo_project_folder s3://${BUCKET}/demo_project_folder
 
 # Replace the default config with the example config
 cp example_project/config.py config.py
 ```
 
 ### Step 1
+
 In config.py you will need to update the following fields specific to your AWS configuration:
-```
+
+```python
 # AWS GENERAL SETTINGS:
 AWS_REGION = 'us-east-1'
 AWS_PROFILE = 'default'                 # The same profile used by your AWS CLI installation
@@ -32,17 +36,21 @@ AWS_BUCKET = 'your-bucket-name'
 SOURCE_BUCKET = 'your-bucket-name'      # Only differs from AWS_BUCKET with advanced configuration
 DESTINATION_BUCKET = 'your-bucket-name' # Only differs from AWS_BUCKET with advanced configuration
 ```
+
 Then run `python3 run.py setup`
 
 ### Step 2
-This command points to the job file created for this demonstartion and should be run as-is.
+
+This command points to the job file created for this demonstration and should be run as-is.
 `python3 run.py submitJob example_project/files/exampleJob.json`
 
 ### Step 3
+
 This command should point to whatever fleet file you created in Step 0 so you may need to update the `exampleFleet.json` file name.
 `python3 run.py startCluster files/exampleFleet.json`
 
 ### Step 4
+
 This command points to the monitor file that is automatically created with your run and should be run as-is.
 `python3 run.py monitor files/FlyExampleSpotFleetRequestId.json`
 
@@ -51,4 +59,23 @@ This command points to the monitor file that is automatically created with your
 While the run is happening, you can watch real-time metrics in your Cloudwatch Dashboard by navigating in the [Cloudwatch console](https://console.aws.amazon.com/cloudwatch).
 Note that the metrics update at intervals that may not be helpful with this fast, minimal example.
 
-After the run is done, you should see your CellProfiler output files in S3 at s3://${BUCKET}/project_folder/output in per-image folders.
\ No newline at end of file
+After the run is done, you should see your CellProfiler output files in S3 at s3://${BUCKET}/project_folder/output in per-image folders.
+
+## Cleanup
+
+The spot fleet, queue, and task definition will be automatically cleaned up after your demo is complete because you are running `monitor`.
+
+To remove everything else:
+
+```bash
+# Remove files added to S3 bucket
+BUCKET=yourbucket
+aws s3 rm --recursive s3://${BUCKET}/demo_project_folder
+
+# Remove Cloudwatch logs
+aws logs delete-log-group --log-group-name FlyExample
+aws logs delete-log-group --log-group-name FlyExample_perInstance
+
+# Delete DeadMessages queue
+aws sqs delete-queue --queue-url ExampleProject_DeadMessages
+```
diff --git a/example_project/project_folder/images/01_POS002_D.TIF b/example_project/demo_project_folder/images/01_POS002_D.TIF
similarity index 100%
rename from example_project/project_folder/images/01_POS002_D.TIF
rename to example_project/demo_project_folder/images/01_POS002_D.TIF
diff --git a/example_project/project_folder/images/01_POS002_F.TIF b/example_project/demo_project_folder/images/01_POS002_F.TIF
similarity index 100%
rename from example_project/project_folder/images/01_POS002_F.TIF
rename to example_project/demo_project_folder/images/01_POS002_F.TIF
diff --git a/example_project/project_folder/images/01_POS002_R.TIF b/example_project/demo_project_folder/images/01_POS002_R.TIF
similarity index 100%
rename from example_project/project_folder/images/01_POS002_R.TIF
rename to example_project/demo_project_folder/images/01_POS002_R.TIF
diff --git a/example_project/project_folder/images/01_POS076_D.TIF b/example_project/demo_project_folder/images/01_POS076_D.TIF
similarity index 100%
rename from example_project/project_folder/images/01_POS076_D.TIF
rename to example_project/demo_project_folder/images/01_POS076_D.TIF
diff --git a/example_project/project_folder/images/01_POS076_F.TIF b/example_project/demo_project_folder/images/01_POS076_F.TIF
similarity index 100%
rename from example_project/project_folder/images/01_POS076_F.TIF
rename to example_project/demo_project_folder/images/01_POS076_F.TIF
diff --git a/example_project/project_folder/images/01_POS076_R.TIF b/example_project/demo_project_folder/images/01_POS076_R.TIF
similarity index 100%
rename from example_project/project_folder/images/01_POS076_R.TIF
rename to example_project/demo_project_folder/images/01_POS076_R.TIF
diff --git a/example_project/project_folder/images/01_POS218_D.TIF b/example_project/demo_project_folder/images/01_POS218_D.TIF
similarity index 100%
rename from example_project/project_folder/images/01_POS218_D.TIF
rename to example_project/demo_project_folder/images/01_POS218_D.TIF
diff --git a/example_project/project_folder/images/01_POS218_F.TIF b/example_project/demo_project_folder/images/01_POS218_F.TIF
similarity index 100%
rename from example_project/project_folder/images/01_POS218_F.TIF
rename to example_project/demo_project_folder/images/01_POS218_F.TIF
diff --git a/example_project/project_folder/images/01_POS218_R.TIF b/example_project/demo_project_folder/images/01_POS218_R.TIF
similarity index 100%
rename from example_project/project_folder/images/01_POS218_R.TIF
rename to example_project/demo_project_folder/images/01_POS218_R.TIF
diff --git a/example_project/project_folder/workspace/ExampleFly.cppipe b/example_project/demo_project_folder/workspace/ExampleFly.cppipe
similarity index 100%
rename from example_project/project_folder/workspace/ExampleFly.cppipe
rename to example_project/demo_project_folder/workspace/ExampleFly.cppipe
diff --git a/example_project/project_folder/workspace/load_data.csv b/example_project/demo_project_folder/workspace/load_data.csv
similarity index 100%
rename from example_project/project_folder/workspace/load_data.csv
rename to example_project/demo_project_folder/workspace/load_data.csv
diff --git a/example_project/files/exampleJob.json b/example_project/files/exampleJob.json
index c1ad5ee..e2c1308 100644
--- a/example_project/files/exampleJob.json
+++ b/example_project/files/exampleJob.json
@@ -1,9 +1,9 @@
 {
   "_comment1": "Paths in this file are relative to the root of your S3 bucket",
-  "pipeline": "project_folder/workspace/ExampleFly.cppipe", 
-  "data_file": "project_folder/workspace/load_data.csv", 
-  "input": "project_folder/workspace/",
-  "output": "project_folder/output",
+  "pipeline": "demo_project_folder/workspace/ExampleFly.cppipe", 
+  "data_file": "demo_project_folder/workspace/load_data.csv", 
+  "input": "demo_project_folder/workspace/",
+  "output": "demo_project_folder/output",
   "output_structure": "Metadata_Position",
   "_comment2": "The following groups are tasks, and each will be run in parallel",
   "groups": [
diff --git a/example_project_CPG/README.md b/example_project_CPG/README.md
new file mode 100644
index 0000000..8fa3506
--- /dev/null
+++ b/example_project_CPG/README.md
@@ -0,0 +1,82 @@
+# CPG Example Project
+
+Included in this folder is all of the resources for running a complete mini-example of Distributed-CellProfiler.
+This example differs from the other example project in that it reads data hosted in the public data repository the [Cell Painting Gallery](https://github.com/broadinstitute/cellpainting-gallery) instead of reading images from your own bucket.
+Workspace files are hosted in your own S3 bucket, and data is output to your bucket, and compute is performed in your account.
+It includes the Distributed-CellProfiler files pre-configured to create a queue of 3 jobs and spin up a spot fleet of 3 instances, each of which will process a single image set.
+
+## Running example project
+
+### Step 0
+
+Before running this mini-example, you will need to set up your AWS infrastructure as described in our [online documentation](https://distributedscience.github.io/Distributed-CellProfiler/step_0_prep.html).
+This includes creating the fleet file that you will use in Step 3.
+
+Upload the 'sample_project' folder to the top level of your bucket.
+While in the `Distributed-CellProfiler` folder, use the following command, replacing `yourbucket` with your bucket name:
+
+```bash
+# Copy example files to S3
+BUCKET=yourbucket
+aws s3 sync example_project_CPG/demo_project_folder s3://${BUCKET}/demo_project_folder
+
+# Replace the default config with the example config
+cp example_project_CPG/config.py config.py
+```
+
+### Step 1
+
+In config.py you will need to update the following fields specific to your AWS configuration:
+
+```python
+# AWS GENERAL SETTINGS:
+AWS_REGION = 'us-east-1'
+AWS_PROFILE = 'default'                 # The same profile used by your AWS CLI installation
+SSH_KEY_NAME = 'your-key-file.pem'      # Expected to be in ~/.ssh
+AWS_BUCKET = 'your-bucket-name'
+WORKSPACE_BUCKET = 'your-bucket-name'   # Only differs from AWS_BUCKET with advanced configuration
+DESTINATION_BUCKET = 'your-bucket-name' # Only differs from AWS_BUCKET with advanced configuration
+```
+
+Then run `python run.py setup`
+
+### Step 2
+
+This command points to the job file created for this demonstration and should be run as-is.
+`python run.py submitJob example_project_CPG/files/exampleCPGJob.json`
+
+### Step 3
+
+This command should point to whatever fleet file you created in Step 0 so you may need to update the `exampleFleet.json` file name.
+`python run.py startCluster files/exampleFleet.json`
+
+### Step 4
+
+This command points to the monitor file that is automatically created with your run and should be run as-is.
+`python run.py monitor files/ExampleCPGSpotFleetRequestId.json`
+
+## Results
+
+While a run is happening, you can watch real-time metrics in your Cloudwatch Dashboard by navigating in the [Cloudwatch console](https://console.aws.amazon.com/cloudwatch).
+Note that the metrics update at intervals that may not be helpful with this fast, minimal example.
+
+After the run is done, you should see your CellProfiler output files in your S3 bucket at s3://${BUCKET}/project_folder/output in per-well-and-site folders.
+
+## Cleanup
+
+The spot fleet, queue, and task definition will be automatically cleaned up after your demo is complete because you are running `monitor`.
+
+To remove everything else:
+
+```bash
+# Remove files added to S3 bucket
+BUCKET=yourbucket
+aws s3 rm --recursive s3://${BUCKET}/demo_project_folder
+
+# Remove Cloudwatch logs
+aws logs delete-log-group --log-group-name ExampleCPG
+aws logs delete-log-group --log-group-name ExampleCPG_perInstance
+
+# Delete DeadMessages queue
+aws sqs delete-queue --queue-url ExampleProject_DeadMessages
+```
diff --git a/example_project_CPG/config.py b/example_project_CPG/config.py
new file mode 100644
index 0000000..4f77e4c
--- /dev/null
+++ b/example_project_CPG/config.py
@@ -0,0 +1,55 @@
+# Constants (User configurable)
+
+APP_NAME = 'ExampleCPG'                # Used to generate derivative names unique to the application.
+
+# DOCKER REGISTRY INFORMATION:
+DOCKERHUB_TAG = 'erinweisbart/distributed-cellprofiler:workspace_bucket'
+
+# AWS GENERAL SETTINGS:
+AWS_REGION = 'us-east-1'
+AWS_PROFILE = 'default'                 # The same profile used by your AWS CLI installation
+SSH_KEY_NAME = 'your-key-file.pem'      # Expected to be in ~/.ssh
+AWS_BUCKET = 'your-bucket-name'         # Bucket to use for logging
+SOURCE_BUCKET = 'cellpainting-gallery'  # Bucket to download image files from 
+WORKSPACE_BUCKET = 'your-bucket-name'   # Bucket to download non-image files from
+DESTINATION_BUCKET = 'your-bucket-name' # Bucket to upload files to
+
+# EC2 AND ECS INFORMATION:
+ECS_CLUSTER = 'default'
+CLUSTER_MACHINES = 3
+TASKS_PER_MACHINE = 1
+MACHINE_TYPE = ['c4.xlarge']
+MACHINE_PRICE = 0.13
+EBS_VOL_SIZE = 22                       # In GB.  Minimum allowed is 22.
+DOWNLOAD_FILES = 'True'
+
+# DOCKER INSTANCE RUNNING ENVIRONMENT:
+DOCKER_CORES = 1                        # Number of CellProfiler processes to run inside a docker container
+CPU_SHARES = DOCKER_CORES * 1024        # ECS computing units assigned to each docker container (1024 units = 1 core)
+MEMORY = 7000                           # Memory assigned to the docker container in MB
+SECONDS_TO_START = 3*60                 # Wait before the next CP process is initiated to avoid memory collisions
+
+# SQS QUEUE INFORMATION:
+SQS_QUEUE_NAME = APP_NAME + 'Queue'
+SQS_MESSAGE_VISIBILITY = 10*60           # Timeout (secs) for messages in flight (average time to be processed)
+SQS_DEAD_LETTER_QUEUE = 'ExampleProject_DeadMessages'
+
+# LOG GROUP INFORMATION:
+LOG_GROUP_NAME = APP_NAME 
+
+# CLOUDWATCH DASHBOARD CREATION
+CREATE_DASHBOARD = 'True'           # Create a dashboard in Cloudwatch for run
+CLEAN_DASHBOARD = 'True'            # Automatically remove dashboard at end of run with Monitor
+
+# REDUNDANCY CHECKS
+CHECK_IF_DONE_BOOL = 'False'  #True or False- should it check if there are a certain number of non-empty files and delete the job if yes?
+EXPECTED_NUMBER_FILES = 7    #What is the number of files that trigger skipping a job?
+MIN_FILE_SIZE_BYTES = 1      #What is the minimal number of bytes an object should be to "count"?
+NECESSARY_STRING = ''        #Is there any string that should be in the file name to "count"?
+
+# PLUGINS
+USE_PLUGINS = 'False'
+UPDATE_PLUGINS = 'False'
+PLUGINS_COMMIT = '' # What commit or version tag do you want to check out?
+INSTALL_REQUIREMENTS = 'False'
+REQUIREMENTS_FILE = '' # Path within the plugins repo to a requirements file
diff --git a/example_project_CPG/demo_project_folder/workspace/ExampleCPG.cppipe b/example_project_CPG/demo_project_folder/workspace/ExampleCPG.cppipe
new file mode 100644
index 0000000..c7bb048
--- /dev/null
+++ b/example_project_CPG/demo_project_folder/workspace/ExampleCPG.cppipe
@@ -0,0 +1,134 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:4
+DateRevision:426
+GitHash:
+ModuleCount:7
+HasImagePlaneDetails:False
+
+LoadData:[module_num:1|svn_version:'Unknown'|variable_revision_number:6|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Input data file location:Default Input Folder sub-folder|Desktop/github/Distributed-CellProfiler/example_project_CPG/project_folder/workspace
+    Name of the file:load_data.csv
+    Load images based on this data?:Yes
+    Base image location:Default Input Folder|
+    Process just a range of rows?:No
+    Rows to process:1,100000
+    Group images by metadata?:Yes
+    Select metadata tags for grouping:Well,Site
+    Rescale intensities?:Yes
+
+IdentifyPrimaryObjects:[module_num:2|svn_version:'Unknown'|variable_revision_number:15|show_window:True|notes:['Identify the nuclei from the DAPI image. ']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:OrigDNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):15,90
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Shape
+    Method to draw dividing lines between clumped objects:Intensity
+    Size of smoothing filter:10
+    Suppress local maxima that are closer than this minimum allowed distance:5
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After declumping only
+    Automatically calculate size of smoothing filter for declumping?:Yes
+    Automatically calculate minimum allowed distance between local maxima?:Yes
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:Yes
+    Threshold setting version:12
+    Threshold strategy:Global
+    Thresholding method:Minimum Cross-Entropy
+    Threshold smoothing scale:1
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.005,1
+    Manual threshold:0.0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Three classes
+    Log transform before thresholding?:No
+    Assign pixels in the middle intensity class to the foreground or the background?:Background
+    Size of adaptive window:10
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2
+    Thresholding method:Otsu
+
+IdentifySecondaryObjects:[module_num:3|svn_version:'Unknown'|variable_revision_number:10|show_window:True|notes:['Identify the cells by using the nuclei as a "seed" region, then growing outwards until stopped by the image threshold or by a neighbor.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input objects:Nuclei
+    Name the objects to be identified:Cells
+    Select the method to identify the secondary objects:Watershed - Image
+    Select the input image:OrigRNA
+    Number of pixels by which to expand the primary objects:10
+    Regularization factor:0.05
+    Discard secondary objects touching the border of the image?:No
+    Discard the associated primary objects?:No
+    Name the new primary objects:FilteredNuclei
+    Fill holes in identified objects?:Yes
+    Threshold setting version:12
+    Threshold strategy:Global
+    Thresholding method:Otsu
+    Threshold smoothing scale:0
+    Threshold correction factor:.7
+    Lower and upper bounds on threshold:0.005,.6
+    Manual threshold:0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Three classes
+    Log transform before thresholding?:Yes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:10
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2
+    Thresholding method:Otsu
+
+IdentifyTertiaryObjects:[module_num:4|svn_version:'Unknown'|variable_revision_number:3|show_window:True|notes:['Identify the cytoplasm by "subtracting" the nuclei objects from the cell objects.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Select the larger identified objects:Cells
+    Select the smaller identified objects:Nuclei
+    Name the tertiary objects to be identified:Cytoplasm
+    Shrink smaller object prior to subtraction?:Yes
+
+MeasureObjectSizeShape:[module_num:5|svn_version:'Unknown'|variable_revision_number:3|show_window:True|notes:['Measure morphological features from the cell, nuclei and cytoplasm objects.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Select object sets to measure:Cells, Nuclei, Cytoplasm
+    Calculate the Zernike features?:Yes
+    Calculate the advanced features?:No
+
+MeasureObjectIntensity:[module_num:6|svn_version:'Unknown'|variable_revision_number:4|show_window:True|notes:['Measure intensity features from nuclei, cell, and cytoplasm objects in all channels']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Select images to measure:OrigAGP, OrigDNA, OrigER, OrigMito, OrigRNA
+    Select objects to measure:Nuclei, Cells, Cytoplasm
+
+ExportToSpreadsheet:[module_num:7|svn_version:'Unknown'|variable_revision_number:13|show_window:True|notes:['Export any measurements to a comma-delimited file (.csv). The measurements made for the nuclei, cell and cytoplasm objects will be saved to separate .csv files, in addition to the per-image .csv’s.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Select the column delimiter:Comma (",")
+    Add image metadata columns to your object data file?:No
+    Add image file and folder names to your object data file?:No
+    Select the measurements to export:No
+    Calculate the per-image mean values for object measurements?:No
+    Calculate the per-image median values for object measurements?:No
+    Calculate the per-image standard deviation values for object measurements?:No
+    Output file location:Default Output Folder|.
+    Create a GenePattern GCT file?:No
+    Select source of sample row name:Metadata
+    Select the image to use as the identifier:None
+    Select the metadata to use as the identifier:None
+    Export all measurement types?:Yes
+    Press button to select measurements:None|None
+    Representation of Nan/Inf:NaN
+    Add a prefix to file names?:No
+    Filename prefix:MyExpt_
+    Overwrite existing files without warning?:Yes
+    Data to export:Image
+    Combine these object measurements with those of the previous object?:No
+    File name:Image.csv
+    Use the object name for the file name?:No
+    Data to export:Nuclei
+    Combine these object measurements with those of the previous object?:No
+    File name:Nuclei.csv
+    Use the object name for the file name?:No
+    Data to export:Cells
+    Combine these object measurements with those of the previous object?:No
+    File name:Cells.csv
+    Use the object name for the file name?:No
+    Data to export:Cytoplasm
+    Combine these object measurements with those of the previous object?:No
+    File name:Cytoplasm.csv
+    Use the object name for the file name?:No
diff --git a/example_project_CPG/demo_project_folder/workspace/load_data.csv b/example_project_CPG/demo_project_folder/workspace/load_data.csv
new file mode 100644
index 0000000..ab86644
--- /dev/null
+++ b/example_project_CPG/demo_project_folder/workspace/load_data.csv
@@ -0,0 +1,217 @@
+Metadata_Source,Metadata_Batch,Metadata_Plate,Metadata_Well,Metadata_Site,FileName_OrigAGP,FileName_OrigDNA,FileName_OrigER,FileName_OrigMito,FileName_OrigRNA,PathName_OrigAGP,PathName_OrigDNA,PathName_OrigER,PathName_OrigMito,PathName_OrigRNA
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\ No newline at end of file
diff --git a/example_project_CPG/files/exampleCPGJob.json b/example_project_CPG/files/exampleCPGJob.json
new file mode 100644
index 0000000..ced422b
--- /dev/null
+++ b/example_project_CPG/files/exampleCPGJob.json
@@ -0,0 +1,15 @@
+{
+  "_comment1": "Paths in this file are relative to the root of your S3 bucket",
+  "pipeline": "demo_project_folder/workspace/ExampleCPG.cppipe", 
+  "data_file": "demo_project_folder/workspace/load_data.csv", 
+  "input": "demo_project_folder/workspace/",
+  "output": "demo_project_folder/output",
+  "output_structure": "Metadata_Well-Metadata_Site",
+  "_comment2": "The following groups are tasks, and each will be run in parallel",
+  "groups": [
+    {"Metadata": "Metadata_Well=A01,Metadata_Site=1"},
+    {"Metadata": "Metadata_Well=A01,Metadata_Site=2"},
+    {"Metadata": "Metadata_Well=A02,Metadata_Site=1"}
+  ]
+}
+
diff --git a/run.py b/run.py
index 371a93f..6ef6a05 100644
--- a/run.py
+++ b/run.py
@@ -11,6 +11,7 @@
 
 # Back compatability with old config versions
 SOURCE_BUCKET = 'False'
+WORKSPACE_BUCKET = 'False'
 UPLOAD_FLAGS = 'False'
 UPDATE_PLUGINS = 'False'
 CREATE_DASHBOARD = 'False'
@@ -124,7 +125,7 @@ def generate_task_definition(AWS_PROFILE):
         {"name": "NECESSARY_STRING", "value": NECESSARY_STRING},
         {"name": "DOWNLOAD_FILES", "value": DOWNLOAD_FILES},
     ]
-    if SOURCE_BUCKET.lower()=='true':
+    if SOURCE_BUCKET.lower()!='false':
         task_definition['containerDefinitions'][0]['environment'] += [
             {
                 'name': 'SOURCE_BUCKET',
@@ -134,7 +135,13 @@ def generate_task_definition(AWS_PROFILE):
                 'name': 'DESTINATION_BUCKET',
                 'value': DESTINATION_BUCKET
             }]
-    if UPLOAD_FLAGS.lower()=='true':
+    if WORKSPACE_BUCKET.lower()!='false':
+        task_definition['containerDefinitions'][0]['environment'] += [
+            {
+                'name': 'WORKSPACE_BUCKET',
+                'value': WORKSPACE_BUCKET
+            }]
+    if UPLOAD_FLAGS.lower()!='false':
         task_definition['containerDefinitions'][0]['environment'] += [
             {
                 'name': 'UPLOAD_FLAGS',
@@ -829,3 +836,4 @@ def monitor(cheapest=False):
         startCluster()
     elif sys.argv[1] == 'monitor':
         monitor()
+        
\ No newline at end of file
diff --git a/worker/cp-worker.py b/worker/cp-worker.py
index f93424e..b2a1c74 100644
--- a/worker/cp-worker.py
+++ b/worker/cp-worker.py
@@ -23,6 +23,10 @@
     DESTINATION_BUCKET = os.environ['AWS_BUCKET']
 else:
     DESTINATION_BUCKET = os.environ['DESTINATION_BUCKET']
+if 'WORKSPACE_BUCKET' not in os.environ:
+    WORKSPACE_BUCKET = os.environ['SOURCE_BUCKET']
+else:
+    WORKSPACE_BUCKET = os.environ['WORKSPACE_BUCKET']
 if 'UPLOAD_FLAGS' in os.environ:
     UPLOAD_FLAGS = os.environ['UPLOAD_FLAGS']
 else:
@@ -39,11 +43,11 @@
 else:
     USE_PLUGINS = os.environ['USE_PLUGINS']
 if 'NECESSARY_STRING' not in os.environ:
-    NECESSARY_STRING = False
+    NECESSARY_STRING = ''
 else:
     NECESSARY_STRING = os.environ['NECESSARY_STRING']
 if 'DOWNLOAD_FILES' not in os.environ:
-    DOWNLOAD_FILES = False
+    DOWNLOAD_FILES = 'False'
 else:
     DOWNLOAD_FILES = os.environ['DOWNLOAD_FILES']
 
@@ -162,97 +166,112 @@ def runCellProfiler(message):
             bucketlist=s3client.list_objects(Bucket=DESTINATION_BUCKET,Prefix=f'{remoteOut}/')
             objectsizelist=[k['Size'] for k in bucketlist['Contents']]
             objectsizelist = [i for i in objectsizelist if i >= MIN_FILE_SIZE_BYTES]
-            if NECESSARY_STRING:
-                if NECESSARY_STRING != '':
-                    objectsizelist = [i for i in objectsizelist if NECESSARY_STRING in i]
+            if NECESSARY_STRING != '':
+                objectsizelist = [i for i in objectsizelist if NECESSARY_STRING in i]
             if len(objectsizelist)>=int(EXPECTED_NUMBER_FILES):
                 printandlog('File not run due to > expected number of files',logger)
                 logger.removeHandler(watchtowerlogger)
                 return 'SUCCESS'
         except KeyError: #Returned if that folder does not exist
             pass	
-    
-    data_file_path = os.path.join(DATA_ROOT,message['data_file'])
 
     downloaded_files = []
 
-    # Optional- download files
-    if DOWNLOAD_FILES:
-        if DOWNLOAD_FILES.lower() == 'true':
-            if not os.path.exists(localIn):
-                os.mkdir(localIn)
-            s3 = boto3.resource('s3')
-            if message['data_file'][-3:]=='.csv':
-                printandlog('Figuring which files to download', logger)
-                import pandas
-                csv_in = pandas.read_csv(data_file_path)
-                csv_in=csv_in.astype('str')
-                #Figure out what metadata fields we need in this experiment, as a dict
-                if type(message['Metadata'])==dict:
-                    filter_dict = message['Metadata']
+    # Optional - download all files, bypass S3 mounting
+    if DOWNLOAD_FILES.lower() == 'true':
+        # Download load data file and image files
+        data_file_path = os.path.join(localIn,message['data_file'])
+        printandlog(f"Downloading {message['data_file']} from {WORKSPACE_BUCKET}", logger)
+        csv_insubfolders = message['data_file'].split('/')
+        subfolders = '/'.join((csv_insubfolders)[:-1])
+        if not os.path.exists(os.path.join(localIn,subfolders)):
+            os.makedirs(os.path.join(localIn,subfolders), exist_ok=True)
+        s3 = boto3.resource('s3')
+        s3.meta.client.download_file(WORKSPACE_BUCKET, message['data_file'], data_file_path)
+        if message['data_file'][-4:]=='.csv':
+            printandlog('Figuring which files to download', logger)
+            import pandas
+            csv_in = pandas.read_csv(data_file_path)
+            csv_in=csv_in.astype('str')
+            #Figure out what metadata fields we need in this experiment, as a dict
+            if type(message['Metadata'])==dict:
+                filter_dict = message['Metadata']
+            else:
+                filter_dict = {}
+                for eachMetadata in message['Metadata'].split(','):
+                    filterkey, filterval = eachMetadata.split('=')
+                    filter_dict[filterkey] = filterval
+            #Filter our CSV to just the rows CellProfiler will process, so that we can download only what we need
+            for eachfilter in filter_dict.keys():
+                csv_in = csv_in[csv_in[eachfilter] == filter_dict[eachfilter]]
+            if len(csv_in) < 1:
+                printandlog('WARNING: All rows filtered out of csv before download. Check your Metadata.',logger)
+                logger.removeHandler(watchtowerlogger)
+                import shutil
+                shutil.rmtree(localOut, ignore_errors=True)
+                return 'INPUT_PROBLEM'
+            #Figure out the actual file names and get them
+            channel_list = [x.split('FileName_')[1] for x in csv_in.columns if 'FileName' in x]
+            printandlog(f'Downloading files for channels {channel_list}', logger)
+            for channel in channel_list:
+                for field in range(csv_in.shape[0]):
+                    full_old_file_name = os.path.join(list(csv_in[f'PathName_{channel}'])[field],list(csv_in[f'FileName_{channel}'])[field])
+                    prefix_on_bucket = full_old_file_name.split(DATA_ROOT)[1][1:]
+                    new_file_name = os.path.join(localIn,prefix_on_bucket)
+                    if not os.path.exists(os.path.split(new_file_name)[0]):
+                        os.makedirs(os.path.split(new_file_name)[0])
+                        printandlog(f'Made directory {os.path.split(new_file_name)[0]}',logger)
+                    if not os.path.exists(new_file_name):
+                        s3.meta.client.download_file(SOURCE_BUCKET,prefix_on_bucket,new_file_name)
+                        downloaded_files.append(new_file_name)
+            printandlog(f'Downloaded {str(len(downloaded_files))} files',logger)
+            import random
+            newtag = False
+            while newtag == False:
+                tag = str(random.randint(100000,999999)) #keep files from overwriting one another
+                local_data_file_path = os.path.join(localIn,tag,os.path.split(data_file_path)[1])
+                if not os.path.exists(local_data_file_path):
+                    if not os.path.exists(os.path.split(local_data_file_path)[0]):
+                        os.makedirs(os.path.split(local_data_file_path)[0])
+                    csv_in = pandas.read_csv(data_file_path)
+                    csv_in.replace(DATA_ROOT,localIn,regex=True, inplace=True)
+                    csv_in.to_csv(local_data_file_path,index=False)
+                    print('Wrote updated CSV')
+                    newtag = True
                 else:
-                    filter_dict = {}
-                    for eachMetadata in message['Metadata'].split(','):
-                        filterkey, filterval = eachMetadata.split('=')
-                        filter_dict[filterkey] = filterval
-                #Filter our CSV to just the rows CellProfiler will process, so that we can download only what we need
-                for eachfilter in filter_dict.keys():
-                    csv_in = csv_in[csv_in[eachfilter] == filter_dict[eachfilter]]
-                if len(csv_in) <= 1:
-                    printandlog('WARNING: All rows filtered out of csv before download. Check your Metadata.')
-                #Figure out the actual file names and get them
-                channel_list = [x.split('FileName_')[1] for x in csv_in.columns if 'FileName' in x]
-                printandlog('Downloading files', logger)
-                for channel in channel_list:
-                    for field in range(csv_in.shape[0]):
-                        full_old_file_name = os.path.join(list(csv_in[f'PathName_{channel}'])[field],list(csv_in[f'FileName_{channel}'])[field])
-                        prefix_on_bucket = full_old_file_name.split(DATA_ROOT)[1][1:]
-                        new_file_name = os.path.join(localIn,prefix_on_bucket)
-                        if not os.path.exists(os.path.split(new_file_name)[0]):
-                            os.makedirs(os.path.split(new_file_name)[0])
-                            printandlog(f'made directory {os.path.split(new_file_name)[0]}',logger)
-                        if not os.path.exists(new_file_name):
-                            s3.meta.client.download_file(AWS_BUCKET,prefix_on_bucket,new_file_name)
-                            downloaded_files.append(new_file_name)
-                printandlog(f'Downloaded {str(len(downloaded_files))} files',logger)
-                import random
-                newtag = False
-                while newtag == False:
-                    tag = str(random.randint(100000,999999)) #keep files from overwriting one another
-                    local_data_file_path = os.path.join(localIn,tag,os.path.split(data_file_path)[1])
-                    if not os.path.exists(local_data_file_path):
-                        if not os.path.exists(os.path.split(local_data_file_path)[0]):
-                            os.makedirs(os.path.split(local_data_file_path)[0])
-                        csv_in = pandas.read_csv(data_file_path)
-                        csv_in.replace(DATA_ROOT,localIn,regex=True, inplace=True)
-                        csv_in.to_csv(local_data_file_path,index=False)
-                        print('Wrote updated CSV')
-                        newtag = True
-                    else:
-                        newtag = False
-                data_file_path = local_data_file_path
-            elif message['data_file'][-3:]=='.txt':
-                printandlog('Downloading files', logger)
-                with open(data_file_path, 'r') as f:
-                    for file_path in f:
-                        prefix_on_bucket = file_path.split(DATA_ROOT)[1][1:]
-                        new_file_name = os.path.join(localIn,prefix_on_bucket)
-                        if not os.path.exists(os.path.split(new_file_name)[0]):
-                            os.makedirs(os.path.split(new_file_name)[0])
-                            printandlog(f'made directory {os.path.split(new_file_name)[0]}',logger)
-                        if not os.path.exists(new_file_name):
-                            s3.meta.client.download_file(AWS_BUCKET,prefix_on_bucket,new_file_name)
-                            downloaded_files.append(new_file_name)
-                printandlog(f'Downloaded {str(len(downloaded_files))} files',logger)
+                    newtag = False
+            data_file_path = local_data_file_path
+        elif message['data_file'][-4:]=='.txt':
+            printandlog('Downloading files', logger)
+            with open(data_file_path, 'r') as f:
+                for file_path in f:
+                    prefix_on_bucket = file_path.split(DATA_ROOT)[1][1:]
+                    new_file_name = os.path.join(localIn,prefix_on_bucket)
+                    if not os.path.exists(os.path.split(new_file_name)[0]):
+                        os.makedirs(os.path.split(new_file_name)[0])
+                        printandlog(f'made directory {os.path.split(new_file_name)[0]}',logger)
+                    if not os.path.exists(new_file_name):
+                        s3.meta.client.download_file(SOURCE_BUCKET,prefix_on_bucket,new_file_name)
+                        downloaded_files.append(new_file_name)
+            printandlog(f'Downloaded {str(len(downloaded_files))} files',logger)
+        else:
+            printandlog("Couldn't parse data file for file download. Not supported input of .csv or .txt",logger)
+        # Download pipeline and update pipeline path in message
+        printandlog(f"Downloading {message['pipeline']} from {WORKSPACE_BUCKET}", logger)
+        pipepath = os.path.join(localIn, message['pipeline'].split('/')[-1])
+        s3.meta.client.download_file(WORKSPACE_BUCKET, message['pipeline'], pipepath)
+    else:
+        data_file_path = os.path.join(DATA_ROOT,message['data_file'])
+        pipepath = os.path.join(DATA_ROOT,message["pipeline"])
 
     # Build and run CellProfiler command
     cpDone = f'{localOut}/cp.is.done'
     if message['data_file'][-4:]=='.csv':
-        cmd = f'cellprofiler -c -r -p {DATA_ROOT}/{message["pipeline"]} -i {DATA_ROOT}/{message["input"]} -o {localOut} -d {cpDone} --data-file={data_file_path} -g {message["Metadata"]}'
+        cmd = f'cellprofiler -c -r -p {pipepath} -i {DATA_ROOT}/{message["input"]} -o {localOut} -d {cpDone} --data-file={data_file_path} -g {message["Metadata"]}'
     elif message['data_file'][-3:]=='.h5':
-        cmd = f'cellprofiler -c -r -p {DATA_ROOT}/{message["pipeline"]} -i {DATA_ROOT}/{message["input"]} -o {localOut} -d {cpDone} -g {message["Metadata"]}'
+        cmd = f'cellprofiler -c -r -p {pipepath} -i {DATA_ROOT}/{message["input"]} -o {localOut} -d {cpDone} -g {message["Metadata"]}'
     elif message['data_file'][-4:]=='.txt':
-        cmd = f'cellprofiler -c -r -p {DATA_ROOT}/{message["pipeline"]} -i {DATA_ROOT}/{message["input"]} -o {localOut} -d {cpDone} --file-list={data_file_path} -g {message["Metadata"]}'
+        cmd = f'cellprofiler -c -r -p {pipepath} -i {DATA_ROOT}/{message["input"]} -o {localOut} -d {cpDone} --file-list={data_file_path} -g {message["Metadata"]}'
     else:
         printandlog("Didn't recognize input file",logger)
     if USE_PLUGINS.lower() == 'true':
@@ -343,4 +362,4 @@ def main():
     logging.basicConfig(level=logging.INFO)
     print('Worker started')
     main()
-    print('Worker finished')
+    print('Worker finished')
\ No newline at end of file