diff --git a/app/controllers/workflow_executions_controller.rb b/app/controllers/workflow_executions_controller.rb
index 83362f1914..a173d410d6 100644
--- a/app/controllers/workflow_executions_controller.rb
+++ b/app/controllers/workflow_executions_controller.rb
@@ -54,7 +54,7 @@ def workflow_execution_params_attributes
 
   def samples_workflow_execution_params_attributes
     [
-      :id,
+      :id, # index, increment for each one, not necissary for functionality
       :sample_id,
       { samplesheet_params: {} }
     ]
diff --git a/app/graphql/mutations/submit_workflow_execution.rb b/app/graphql/mutations/submit_workflow_execution.rb
new file mode 100644
index 0000000000..25743a579c
--- /dev/null
+++ b/app/graphql/mutations/submit_workflow_execution.rb
@@ -0,0 +1,134 @@
+# frozen_string_literal: true
+
+module Mutations
+  # Base Mutation
+  class SubmitWorkflowExecution < BaseMutation # rubocop:disable Metrics/ClassLength
+    null true
+    description 'Create a new workflow execution..'
+
+    argument :email_notification,
+             Boolean,
+             required: false,
+             default_value: false,
+             description: 'Set to true to enable email notifications from this workflow execution'
+    argument :name, String, required: false, description: 'Name for the new workflow.'
+    argument :samples_workflow_executions_attributes, [GraphQL::Types::JSON], description: "A list of hashes containing a 'sample_id', and a hash of `samplesheet_params`." # rubocop:disable GraphQL/ExtractInputType,Layout/LineLength
+    argument :update_samples, # rubocop:disable GraphQL/ExtractInputType
+             Boolean,
+             required: false,
+             default_value: false,
+             description: 'Set true for samples to be updated from this workflow execution'
+    argument :workflow_engine, String, description: '' # rubocop:disable GraphQL/ExtractInputType
+    argument :workflow_engine_parameters, [GraphQL::Types::JSON], description: 'List of Hashes containing `key` and `value` to be passed to the workflow engine.' # rubocop:disable GraphQL/ExtractInputType,Layout/LineLength
+    argument :workflow_engine_version, String, description: 'Workflow Engine Version' # rubocop:disable GraphQL/ExtractInputType
+    argument :workflow_name, String, description: 'Name of the pipeline to be run on this workflow execution' # rubocop:disable GraphQL/ExtractInputType
+    argument :workflow_params, GraphQL::Types::JSON, description: 'Parameters to be passed to the pipeline.' # rubocop:disable GraphQL/ExtractInputType
+    argument :workflow_type, String, description: 'Type of pipelines workflow.' # rubocop:disable GraphQL/ExtractInputType
+    argument :workflow_type_version, String, description: 'Version of the pipelines workflow type.' # rubocop:disable GraphQL/ExtractInputType
+    argument :workflow_url, String, description: 'Url for the pipeline.' # rubocop:disable GraphQL/ExtractInputType
+    argument :workflow_version, String, description: 'Version of the pipeline to be run on this workflow execution' # rubocop:disable GraphQL/ExtractInputType
+
+    # one of project/group, to use as the namespace
+    argument :project_id, ID, # rubocop:disable GraphQL/ExtractInputType
+             required: false,
+             description: 'The Node ID of the project to run workflow in. For example, `gid://irida/Project/a84cd757-dedb-4c64-8b01-097020163077`.' # rubocop:disable Layout/LineLength
+    argument :group_id, ID, # rubocop:disable GraphQL/OrderedArguments,GraphQL/ExtractInputType
+             required: false,
+             description: 'The Node ID of the group to run workflow in. For example, `gid://irida/Group/a84cd757-dedb-4c64-8b01-097020163077`.' # rubocop:disable Layout/LineLength
+    validates required: { one_of: %i[project_id group_id] }
+
+    field :errors, [Types::UserErrorType], null: false, description: 'A list of errors that prevented the mutation.'
+    field :workflow_execution, Types::WorkflowExecutionType, description: 'The newly created workflow execution.'
+
+    def resolve(args)
+      create_workflow_execution(args)
+    end
+
+    def ready?(**_args)
+      authorize!(to: :mutate?, with: GraphqlPolicy, context: { user: context[:current_user], token: context[:token] })
+    end
+
+    private
+
+    def create_workflow_execution(args) # rubocop:disable Metrics/MethodLength,Metrics/AbcSize
+      workflow_engine_parameters = build_workflow_engine_parameters(args[:workflow_engine_parameters])
+
+      update_samples = args[:update_samples] ? '1' : '0'
+      email_notification = args[:email_notification] ? '1' : '0'
+
+      namespace_id = namespace(args[:project_id], args[:group_id])
+
+      samples_workflow_executions_attributes = build_samples_workflow_executions_attributes(args[:samples_workflow_executions_attributes]) # rubocop:disable Layout/LineLength
+
+      workflow_execution_params = {
+        name: args[:name],
+        metadata: { workflow_name: args[:workflow_name],
+                    workflow_version: args[:workflow_version] },
+        namespace_id:,
+        workflow_params: args[:workflow_params],
+        workflow_type: args[:workflow_type],
+        workflow_type_version: args[:workflow_type_version],
+        workflow_engine: args[:workflow_engine],
+        workflow_engine_version: args[:workflow_engine_version],
+        workflow_engine_parameters:,
+        workflow_url: args[:workflow_url],
+        update_samples:,
+        email_notification:,
+        samples_workflow_executions_attributes:
+      }
+
+      workflow_execution = WorkflowExecutions::CreateService.new(
+        current_user, workflow_execution_params
+      ).execute
+
+      if workflow_execution.persisted?
+        {
+          workflow_execution:,
+          errors: []
+        }
+      else
+        user_errors = workflow_execution.errors.map do |error|
+          {
+            path: ['workflow_execution', error.attribute.to_s.camelize(:lower)],
+            message: error.message
+          }
+        end
+        {
+          workflow_execution: nil,
+          errors: user_errors
+        }
+      end
+    end
+
+    def namespace(project_id, group_id)
+      if project_id
+        IridaSchema.object_from_id(project_id, { expected_type: Project }).namespace.id
+      else # group_id
+        IridaSchema.object_from_id(group_id, { expected_type: Group }).id
+      end
+    end
+
+    # workflow engine parameters can have keys that start with `-` which is not allowed in graphql,
+    # so we parse a list of key value pairs into a hash that can be used.
+    def build_workflow_engine_parameters(parameter_list)
+      result = {}
+      parameter_list.each do |params|
+        result[params['key']] = params['value']
+      end
+      result
+    end
+
+    def build_samples_workflow_executions_attributes(samples_workflow_executions_attributes)
+      result = {}
+      samples_workflow_executions_attributes.each_with_index do |data, index|
+        sample_id = IridaSchema.object_from_id(data['sample_id'], { expected_type: Sample }).id
+        result[index.to_s] = {
+          'sample_id' => sample_id,
+          'samplesheet_params' => data['samplesheet_params']
+        }
+      end
+
+      result
+    end
+  end
+end
diff --git a/app/graphql/schema.graphql b/app/graphql/schema.graphql
index 360d4fdb42..86e4026a0e 100644
--- a/app/graphql/schema.graphql
+++ b/app/graphql/schema.graphql
@@ -1416,6 +1416,16 @@ type Mutation {
     input: CreateSampleInput!
   ): CreateSamplePayload
 
+  """
+  Create a new workflow execution..
+  """
+  submitWorkflowExecution(
+    """
+    Parameters for SubmitWorkflowExecution
+    """
+    input: SubmitWorkflowExecutionInput!
+  ): SubmitWorkflowExecutionPayload
+
   """
   Transfer a list of sample to another project.
   """
@@ -2857,6 +2867,111 @@ type SamplesWorkflowExecution implements Node {
   workflowExecution: WorkflowExecution
 }
 
+"""
+Autogenerated input type of SubmitWorkflowExecution
+"""
+input SubmitWorkflowExecutionInput {
+  """
+  A unique identifier for the client performing the mutation.
+  """
+  clientMutationId: String
+
+  """
+  Set to true to enable email notifications from this workflow execution
+  """
+  emailNotification: Boolean = false
+
+  """
+  The Node ID of the group to run workflow in. For example, `gid://irida/Group/a84cd757-dedb-4c64-8b01-097020163077`.
+  """
+  groupId: ID
+
+  """
+  Name for the new workflow.
+  """
+  name: String
+
+  """
+  The Node ID of the project to run workflow in. For example, `gid://irida/Project/a84cd757-dedb-4c64-8b01-097020163077`.
+  """
+  projectId: ID
+
+  """
+  A list of hashes containing a 'sample_id', and a hash of `samplesheet_params`.
+  """
+  samplesWorkflowExecutionsAttributes: [JSON!]!
+
+  """
+  Set true for samples to be updated from this workflow execution
+  """
+  updateSamples: Boolean = false
+
+  """
+  
+  """
+  workflowEngine: String!
+
+  """
+  List of Hashes containing `key` and `value` to be passed to the workflow engine.
+  """
+  workflowEngineParameters: [JSON!]!
+
+  """
+  Workflow Engine Version
+  """
+  workflowEngineVersion: String!
+
+  """
+  Name of the pipeline to be run on this workflow execution
+  """
+  workflowName: String!
+
+  """
+  Parameters to be passed to the pipeline.
+  """
+  workflowParams: JSON!
+
+  """
+  Type of pipelines workflow.
+  """
+  workflowType: String!
+
+  """
+  Version of the pipelines workflow type.
+  """
+  workflowTypeVersion: String!
+
+  """
+  Url for the pipeline.
+  """
+  workflowUrl: String!
+
+  """
+  Version of the pipeline to be run on this workflow execution
+  """
+  workflowVersion: String!
+}
+
+"""
+Autogenerated return type of SubmitWorkflowExecution.
+"""
+type SubmitWorkflowExecutionPayload {
+  """
+  A unique identifier for the client performing the mutation.
+  """
+  clientMutationId: String
+
+  """
+  A list of errors that prevented the mutation.
+  """
+  errors: [UserError!]!
+
+  """
+  The newly created workflow execution.
+  """
+  workflowExecution: WorkflowExecution
+}
+
 """
 Autogenerated input type of TransferSamples
 """
diff --git a/app/graphql/types/mutation_type.rb b/app/graphql/types/mutation_type.rb
index ba119d5073..498873821f 100644
--- a/app/graphql/types/mutation_type.rb
+++ b/app/graphql/types/mutation_type.rb
@@ -13,6 +13,7 @@ class MutationType < Types::BaseObject
     field :create_group, mutation: Mutations::CreateGroup # rubocop:disable GraphQL/FieldDescription
     field :create_project, mutation: Mutations::CreateProject # rubocop:disable GraphQL/FieldDescription
     field :create_sample, mutation: Mutations::CreateSample # rubocop:disable GraphQL/FieldDescription,GraphQL/ExtractType
+    field :submit_workflow_execution, mutation: Mutations::SubmitWorkflowExecution # rubocop:disable GraphQL/FieldDescription
     field :transfer_samples, mutation: Mutations::TransferSamples # rubocop:disable GraphQL/FieldDescription
     field :update_sample_metadata, mutation: Mutations::UpdateSampleMetadata # rubocop:disable GraphQL/FieldDescription
   end
diff --git a/app/models/samples_workflow_execution.rb b/app/models/samples_workflow_execution.rb
index 7040e5fdcf..082413262e 100644
--- a/app/models/samples_workflow_execution.rb
+++ b/app/models/samples_workflow_execution.rb
@@ -9,4 +9,6 @@ class SamplesWorkflowExecution < ApplicationRecord
   belongs_to :sample
   has_many_attached :inputs
   has_many :outputs, dependent: :destroy, class_name: 'Attachment', as: :attachable
+
+  validates_with WorkflowExecutionSamplesheetParamsValidator
 end
diff --git a/app/models/workflow_execution.rb b/app/models/workflow_execution.rb
index 54102bd15e..c3663fdcee 100644
--- a/app/models/workflow_execution.rb
+++ b/app/models/workflow_execution.rb
@@ -40,7 +40,7 @@ def send_email
   end
 
   def cancellable?
-    %w[submitted running prepared initial].include?(state) 
+    %w[submitted running prepared initial].include?(state)
   end
 
   def deletable?
diff --git a/app/validators/workflow_execution_samplesheet_params_validator.rb b/app/validators/workflow_execution_samplesheet_params_validator.rb
new file mode 100644
index 0000000000..0829a0197c
--- /dev/null
+++ b/app/validators/workflow_execution_samplesheet_params_validator.rb
@@ -0,0 +1,39 @@
+# frozen_string_literal: true
+
+# Validator for Workflow Execution Samplesheet Params
+# This will cause the validation to fail if any of the attachment ids cannot be resolved
+class WorkflowExecutionSamplesheetParamsValidator < ActiveModel::Validator
+  def validate(record) # rubocop:disable Metrics/MethodLength,Metrics/AbcSize,Metrics/CyclomaticComplexity,Metrics/PerceivedComplexity
+    record.samplesheet_params.each do |key, value| # rubocop:disable Metrics/BlockLength
+      if key == 'sample'
+        if value.nil? || value == ''
+          error_message = 'No Sample PUID provided'
+          record.errors.add :sample, error_message
+          record.workflow_execution.errors.add :sample, error_message
+        elsif value != (record.sample.puid)
+          error_message = "Provided Sample PUID #{value} does not match SampleWorkflowExecution Sample PUID #{record.sample.puid}" # rubocop:disable Layout/LineLength
+          record.errors.add :sample, error_message
+          record.workflow_execution.errors.add :sample, error_message
+        end
+        next
+      end
+
+      next if value == ''
+
+      begin
+        # Attempt to parse an object from the id provided
+        attachment = IridaSchema.object_from_id(value, { expected_type: Attachment })
+        unless attachment.attachable == record.sample
+          error_message = "Attachment does not belong to Sample #{record.sample.puid}."
+          record.errors.add :attachment, error_message
+          record.workflow_execution.errors.add :attachment, error_message
+        end
+      rescue StandardError => e
+        error_message = e.message
+        record.errors.add :attachment, error_message
+        record.workflow_execution.errors.add :attachment, error_message
+        next
+      end
+    end
+  end
+end
diff --git a/db/seeds.rb b/db/seeds.rb
index f549d04149..f2483ddd3e 100644
--- a/db/seeds.rb
+++ b/db/seeds.rb
@@ -166,7 +166,15 @@ def seed_workflow_executions # rubocop:disable Metrics/MethodLength, Metrics/Abc
     workflow_engine_version: '23.10.0',
     workflow_engine_parameters: { '-r': 'dev' },
     workflow_url: 'https://github.com/phac-nml/iridanextexample',
-    submitter: User.find_by(email: 'user1@email.com')
+    submitter: User.find_by(email: 'user1@email.com'),
+    samples_workflow_executions_attributes: {
+      '0': {
+        sample_id: Sample.first.id,
+        samplesheet_params: {
+          sample: Sample.first.puid
+        }
+      }
+    }
   )
 
   SamplesWorkflowExecution.create(
@@ -188,7 +196,15 @@ def seed_workflow_executions # rubocop:disable Metrics/MethodLength, Metrics/Abc
     workflow_url: 'https://github.com/phac-nml/iridanextexample',
     submitter: User.find_by(email: 'user1@email.com'),
     blob_run_directory: 'this should be a generated key',
-    state: :completed
+    state: :completed,
+    samples_workflow_executions_attributes: {
+      '0': {
+        sample_id: Sample.first.id,
+        samplesheet_params: {
+          sample: Sample.first.puid
+        }
+      }
+    }
   )
 
   filename = 'summary.txt'
@@ -197,7 +213,6 @@ def seed_workflow_executions # rubocop:disable Metrics/MethodLength, Metrics/Abc
   attachment.save!
 
   SamplesWorkflowExecution.create(
-    samplesheet_params: { my_key1: 'my_value_2', my_key2: 'my_value_3' },
     sample: Sample.first,
     workflow_execution: workflow_execution_completed
   )
diff --git a/test/controllers/workflow_executions_controller_test.rb b/test/controllers/workflow_executions_controller_test.rb
index 17388440b7..4c00eb9eee 100644
--- a/test/controllers/workflow_executions_controller_test.rb
+++ b/test/controllers/workflow_executions_controller_test.rb
@@ -30,7 +30,7 @@ class WorkflowExecutionsControllerTest < ActionDispatch::IntegrationTest
                  {
                    sample_id: @sample1.id,
                    samplesheet_params: {
-                     sample: "Sample_#{@sample1.id}",
+                     sample: @sample1.puid,
                      'fastq_1' => @attachment1.to_global_id,
                      'fastq_2' => ''
                    }
diff --git a/test/fixtures/samples_workflow_executions.yml b/test/fixtures/samples_workflow_executions.yml
index 7fe93badfa..fa0059b5eb 100644
--- a/test/fixtures/samples_workflow_executions.yml
+++ b/test/fixtures/samples_workflow_executions.yml
@@ -5,23 +5,44 @@ samples_workflow_executions_valid:
   workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:workflow_execution_valid, :uuid) %>
   samplesheet_params:
     {
-      key_c: 'value_c'
+      "sample": INXT_SAM_AAAAAAAAAA,
+      "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment1, :uuid)}" %>
     }
 
-samples_workflow_executions_invalid_no_sample:
-  sample_id: null
+samples_workflow_executions_invalid_no_sample_puid:
+  sample_id: <%= ActiveRecord::FixtureSet.identify(:sample1, :uuid) %>
+  workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:workflow_execution_valid, :uuid) %>
+  samplesheet_params:
+    {
+      "sample": '',
+      "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment1, :uuid)}" %>
+    }
+
+samples_workflow_executions_invalid_mismatch_sample_puid:
+  sample_id: <%= ActiveRecord::FixtureSet.identify(:sample1, :uuid) %>
+  workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:workflow_execution_valid, :uuid) %>
+  samplesheet_params:
+    {
+      "sample": INXT_SAM_AAAAAAAAAB,
+      "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment1, :uuid)}" %>
+    }
+
+samples_workflow_executions_invalid_file_id:
+  sample_id: <%= ActiveRecord::FixtureSet.identify(:sample1, :uuid) %>
   workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:workflow_execution_valid, :uuid) %>
   samplesheet_params:
     {
-      key_c: 'value_c'
+      "sample": INXT_SAM_AAAAAAAAAA,
+      "fastq_1": 12345
     }
 
-samples_workflow_executions_invalid_no_workflow_execution:
+samples_workflow_executions_mismatch_file_id:
   sample_id: <%= ActiveRecord::FixtureSet.identify(:sample1, :uuid) %>
-  workflow_execution_id: null
+  workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:workflow_execution_valid, :uuid) %>
   samplesheet_params:
     {
-      key_c: 'value_c'
+      "sample": INXT_SAM_AAAAAAAAAA,
+      "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachmentA, :uuid)}" %>
     }
 
 sample1_irida_next_example:
@@ -117,92 +138,42 @@ sample1_irida_next_example_new:
 sample41_irida_next_example_completing_c:
   sample_id: <%= ActiveRecord::FixtureSet.identify(:sample41, :uuid) %>
   workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:irida_next_example_completing_c, :uuid) %>
-  samplesheet_params: {
-    "sample": INXT_SAM_AAAAAAAABQ,
-    "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment1, :uuid)}" %>,
-    "fastq_2": ""
-  }
 
 sample42_irida_next_example_completing_c:
   sample_id: <%= ActiveRecord::FixtureSet.identify(:sample42, :uuid) %>
   workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:irida_next_example_completing_c, :uuid) %>
-  samplesheet_params: {
-    "sample": INXT_SAM_AAAAAAAABR,
-    "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment2, :uuid)}" %>,
-    "fastq_2": ""
-  }
 
 sample41_irida_next_example_completing_d:
   sample_id: <%= ActiveRecord::FixtureSet.identify(:sample41, :uuid) %>
   workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:irida_next_example_completing_d, :uuid) %>
-  samplesheet_params: {
-    "sample": INXT_SAM_AAAAAAAABQ,
-    "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment1, :uuid)}" %>,
-    "fastq_2": ""
-  }
 
 sample42_irida_next_example_completing_d:
   sample_id: <%= ActiveRecord::FixtureSet.identify(:sample42, :uuid) %>
   workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:irida_next_example_completing_d, :uuid) %>
-  samplesheet_params: {
-    "sample": INXT_SAM_AAAAAAAABR,
-    "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment2, :uuid)}" %>,
-    "fastq_2": ""
-  }
 
 sample41_irida_next_example_completing_e:
   sample_id: <%= ActiveRecord::FixtureSet.identify(:sample41, :uuid) %>
   workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:irida_next_example_completing_e, :uuid) %>
-  samplesheet_params: {
-    "sample": <%= "Sample_#{ActiveRecord::FixtureSet.identify(:sample41, :uuid)}" %>,
-    "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment1, :uuid)}" %>,
-    "fastq_2": ""
-  }
 
 sample42_irida_next_example_completing_e:
   sample_id: <%= ActiveRecord::FixtureSet.identify(:sample42, :uuid) %>
   workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:irida_next_example_completing_e, :uuid) %>
-  samplesheet_params: {
-    "sample": <%= "Sample_#{ActiveRecord::FixtureSet.identify(:sample42, :uuid)}" %>,
-    "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment2, :uuid)}" %>,
-    "fastq_2": ""
-  }
 
 sample41_irida_next_example_completing_f:
   sample_id: <%= ActiveRecord::FixtureSet.identify(:sample41, :uuid) %>
   workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:irida_next_example_completing_f, :uuid) %>
-  samplesheet_params: {
-    "sample": INXT_SAM_AAAAAAAABQ,
-    "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment1, :uuid)}" %>,
-    "fastq_2": ""
-  }
 
 sample42_irida_next_example_completing_f:
   sample_id: <%= ActiveRecord::FixtureSet.identify(:sample42, :uuid) %>
   workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:irida_next_example_completing_f, :uuid) %>
-  samplesheet_params: {
-    "sample": INXT_SAM_AAAAAAAABR,
-    "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment2, :uuid)}" %>,
-    "fastq_2": ""
-  }
 
 sampleA_irida_next_example_completing_g:
   sample_id: <%= ActiveRecord::FixtureSet.identify(:sampleA, :uuid) %>
   workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:irida_next_example_completing_g, :uuid) %>
-  samplesheet_params: {
-    "sample": INXT_SAM_AAAAAAAAA3,
-    "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment1, :uuid)}" %>,
-    "fastq_2": ""
-  }
 
 sampleB_irida_next_example_completing_g:
   sample_id: <%= ActiveRecord::FixtureSet.identify(:sampleB, :uuid) %>
   workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:irida_next_example_completing_g, :uuid) %>
-  samplesheet_params: {
-    "sample": INXT_SAM_AAAAAAAAA4,
-    "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment2, :uuid)}" %>,
-    "fastq_2": ""
-  }
 
 sample46_irida_next_example_completed_with_output:
   sample_id: <%= ActiveRecord::FixtureSet.identify(:sample46, :uuid) %>
@@ -340,3 +311,39 @@ sample_canceled_unclean_DELETE:
     "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment_canceled_unclean_DELETE, :uuid)}" %>,
     "fastq_2": ""
   }
+
+samples_workflow_execution_invalid_metadata:
+  sample_id: <%= ActiveRecord::FixtureSet.identify(:sample1, :uuid) %>
+  workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:workflow_execution_invalid_metadata, :uuid) %>
+  samplesheet_params:
+    {
+      "sample": INXT_SAM_AAAAAAAAAA,
+      "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment1, :uuid)}" %>
+    }
+
+samples_irida_next_example_completing_a:
+  sample_id: <%= ActiveRecord::FixtureSet.identify(:sample1, :uuid) %>
+  workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:irida_next_example_completing_a, :uuid) %>
+  samplesheet_params:
+    {
+      "sample": "INXT_SAM_AAAAAAAAAA",
+      "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment1, :uuid)}" %>
+    }
+
+samples_automated_example_prepared:
+  sample_id: <%= ActiveRecord::FixtureSet.identify(:sample1, :uuid) %>
+  workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:automated_example_prepared, :uuid) %>
+  samplesheet_params:
+    {
+      "sample": INXT_SAM_AAAAAAAAAA,
+      "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment1, :uuid)}" %>
+    }
+
+samples_automated_workflow_execution:
+  sample_id: <%= ActiveRecord::FixtureSet.identify(:sample1, :uuid) %>
+  workflow_execution_id: <%= ActiveRecord::FixtureSet.identify(:automated_workflow_execution, :uuid) %>
+  samplesheet_params:
+    {
+      "sample": INXT_SAM_AAAAAAAAAA,
+      "fastq_1": <%= "gid://irida/Attachment/#{ActiveRecord::FixtureSet.identify(:attachment1, :uuid)}" %>
+    }
diff --git a/test/graphql/submit_workflow_execution_mutation_test.rb b/test/graphql/submit_workflow_execution_mutation_test.rb
new file mode 100644
index 0000000000..19865e2648
--- /dev/null
+++ b/test/graphql/submit_workflow_execution_mutation_test.rb
@@ -0,0 +1,180 @@
+# frozen_string_literal: true
+
+require 'test_helper'
+
+class SubmitWorkflowExecutionMutationTest < ActiveSupport::TestCase
+  SUBMIT_WORKFLOW_EXECUTION_MUTATION = <<~GRAPHQL
+    mutation(
+      $name: String!,
+      $project_id: ID!,
+      $samples_workflow_executions_attributes: [JSON!]!
+      ) {
+      submitWorkflowExecution( input:{
+        name: $name
+        projectId: $project_id
+        updateSamples: false
+        emailNotification: false
+        workflowName: "phac-nml/iridanextexample"
+        workflowVersion: "1.0.3"
+        workflowParams: {
+          assembler: "stub",
+          random_seed: 1,
+          project_name: "assembly"
+        }
+        workflowType: "NFL"
+        workflowTypeVersion:"DSL2"
+        workflowEngine:"nextflow"
+        workflowEngineVersion: "23.10.0"
+        workflowEngineParameters: [
+          {
+            key:"-r",
+            value:"1.0.3"
+          }
+        ]
+        workflowUrl: "https://github.com/phac-nml/iridanextexample"
+        samplesWorkflowExecutionsAttributes: $samples_workflow_executions_attributes
+        }) {
+        workflowExecution{
+          name
+          id
+        }
+        errors{
+          message
+          path
+        }
+      }
+    }
+  GRAPHQL
+
+  def setup
+    @user = users(:john_doe)
+    @project = projects(:project1)
+    @sample = samples(:sample1)
+    @attachment1 = attachments(:attachment1)
+    @attachment2 = attachments(:attachment2)
+  end
+
+  test 'submit workflow execution mutation should work' do
+    samples_workflow_executions_attributes = [
+      {
+        sample_id: @sample.to_global_id.to_s,
+        samplesheet_params: {
+          sample: @sample.puid,
+          fastq_1: @attachment1.to_global_id.to_s, # rubocop:disable Naming/VariableNumber
+          fastq_2: @attachment2.to_global_id.to_s # rubocop:disable Naming/VariableNumber
+        }
+      }
+    ]
+
+    result = IridaSchema.execute(SUBMIT_WORKFLOW_EXECUTION_MUTATION,
+                                 context: { current_user: @user },
+                                 variables: {
+                                   name: 'my_new_workflow_submission',
+                                   project_id: @project.to_global_id.to_s,
+                                   samples_workflow_executions_attributes:
+                                 })
+
+    assert_nil result['errors'], 'should work and have no errors.'
+
+    data = result['data']['submitWorkflowExecution']
+    assert_not_empty data, 'submit workflow execution type should work'
+    workflow_execution = data['workflowExecution']
+    assert_equal 'my_new_workflow_submission', workflow_execution['name']
+  end
+
+  test 'submit workflow execution mutation with non gid project' do
+    samples_workflow_executions_attributes = [
+      {
+        sample_id: @sample.to_global_id.to_s,
+        samplesheet_params: {
+          sample: @sample.puid,
+          fastq_1: @attachment1.to_global_id.to_s, # rubocop:disable Naming/VariableNumber
+          fastq_2: @attachment2.to_global_id.to_s # rubocop:disable Naming/VariableNumber
+        }
+      }
+    ]
+
+    result = IridaSchema.execute(SUBMIT_WORKFLOW_EXECUTION_MUTATION,
+                                 context: { current_user: @user },
+                                 variables: {
+                                   name: 'my_new_workflow_submission',
+                                   project_id: 'not a gid',
+                                   samples_workflow_executions_attributes:
+                                 })
+
+    assert_not_empty result['errors'], 'should have errors.'
+    assert_equal 'not a gid is not a valid IRIDA Next ID.', result['errors'][0]['message']
+  end
+
+  test 'submit workflow execution mutation with non project gid' do
+    samples_workflow_executions_attributes = [
+      {
+        sample_id: @sample.to_global_id.to_s,
+        samplesheet_params: {
+          sample: @sample.puid,
+          fastq_1: @attachment1.to_global_id.to_s, # rubocop:disable Naming/VariableNumber
+          fastq_2: @attachment2.to_global_id.to_s # rubocop:disable Naming/VariableNumber
+        }
+      }
+    ]
+
+    result = IridaSchema.execute(SUBMIT_WORKFLOW_EXECUTION_MUTATION,
+                                 context: { current_user: @user },
+                                 variables: {
+                                   name: 'my_new_workflow_submission',
+                                   project_id: @sample.to_global_id.to_s,
+                                   samples_workflow_executions_attributes:
+                                 })
+
+    assert_not_empty result['errors'], 'should have errors.'
+    assert_equal "#{@sample.to_global_id} is not a valid ID for Project", result['errors'][0]['message']
+  end
+
+  test 'submit workflow execution mutation should fail with invalid sample gid' do
+    samples_workflow_executions_attributes = [
+      {
+        sample_id: 'this is not a gid',
+        samplesheet_params: {
+          sample: @sample.puid,
+          fastq_1: @attachment1.to_global_id.to_s, # rubocop:disable Naming/VariableNumber
+          fastq_2: @attachment2.to_global_id.to_s # rubocop:disable Naming/VariableNumber
+        }
+      }
+    ]
+
+    result = IridaSchema.execute(SUBMIT_WORKFLOW_EXECUTION_MUTATION,
+                                 context: { current_user: @user },
+                                 variables: {
+                                   name: 'my_new_workflow_submission',
+                                   project_id: @project.to_global_id.to_s,
+                                   samples_workflow_executions_attributes:
+                                 })
+
+    assert_not_empty result['errors'], 'should have errors.'
+    assert_equal 'this is not a gid is not a valid IRIDA Next ID.', result['errors'][0]['message']
+  end
+
+  test 'submit workflow execution mutation should fail with non sample gid' do
+    samples_workflow_executions_attributes = [
+      {
+        sample_id: @project.to_global_id.to_s,
+        samplesheet_params: {
+          sample: @sample.puid,
+          fastq_1: @attachment1.to_global_id.to_s, # rubocop:disable Naming/VariableNumber
+          fastq_2: @attachment2.to_global_id.to_s # rubocop:disable Naming/VariableNumber
+        }
+      }
+    ]
+
+    result = IridaSchema.execute(SUBMIT_WORKFLOW_EXECUTION_MUTATION,
+                                 context: { current_user: @user },
+                                 variables: {
+                                   name: 'my_new_workflow_submission',
+                                   project_id: @project.to_global_id.to_s,
+                                   samples_workflow_executions_attributes:
+                                 })
+
+    assert_not_empty result['errors'], 'should have errors.'
+    assert_equal "#{@project.to_global_id} is not a valid ID for Sample", result['errors'][0]['message']
+  end
+end
diff --git a/test/models/samples_workflow_executions_test.rb b/test/models/samples_workflow_executions_test.rb
index 5316cb5991..99b83af4e7 100644
--- a/test/models/samples_workflow_executions_test.rb
+++ b/test/models/samples_workflow_executions_test.rb
@@ -7,11 +7,17 @@ def setup
     @samples_workflow_executions_valid = samples_workflow_executions(
       :samples_workflow_executions_valid
     )
-    @samples_workflow_executions_invalid_no_sample = samples_workflow_executions(
-      :samples_workflow_executions_invalid_no_sample
+    @samples_workflow_executions_invalid_no_sample_puid = samples_workflow_executions(
+      :samples_workflow_executions_invalid_no_sample_puid
     )
-    @samples_workflow_executions_invalid_no_workflow_execution = samples_workflow_executions(
-      :samples_workflow_executions_invalid_no_workflow_execution
+    @samples_workflow_executions_invalid_mismatch_sample_puid = samples_workflow_executions(
+      :samples_workflow_executions_invalid_mismatch_sample_puid
+    )
+    @samples_workflow_executions_invalid_file_id = samples_workflow_executions(
+      :samples_workflow_executions_invalid_file_id
+    )
+    @samples_workflow_executions_mismatch_file_id = samples_workflow_executions(
+      :samples_workflow_executions_mismatch_file_id
     )
   end
 
@@ -19,18 +25,37 @@ def setup
     assert @samples_workflow_executions_valid.valid?
   end
 
-  test 'invalid no sample' do
-    assert_not @samples_workflow_executions_invalid_no_sample.valid?
-    assert_not_nil @samples_workflow_executions_invalid_no_sample.errors
-    assert_equal ['Sample must exist'], @samples_workflow_executions_invalid_no_sample.errors.full_messages
+  test 'invalid mismatch puid' do
+    assert_not @samples_workflow_executions_invalid_mismatch_sample_puid.valid?
+    assert_not_nil @samples_workflow_executions_invalid_mismatch_sample_puid.errors
+    expected_error = 'Sample Provided Sample PUID INXT_SAM_AAAAAAAAAB does not match SampleWorkflowExecution Sample PUID INXT_SAM_AAAAAAAAAA' # rubocop:disable Layout/LineLength
+    assert_equal expected_error, @samples_workflow_executions_invalid_mismatch_sample_puid.errors.full_messages[0]
+  end
+
+  test 'invalid no sample puid' do
+    assert_not @samples_workflow_executions_invalid_no_sample_puid.valid?
+    assert_not_nil @samples_workflow_executions_invalid_no_sample_puid.errors
+    expected_error = 'Sample No Sample PUID provided'
+    assert_equal expected_error, @samples_workflow_executions_invalid_no_sample_puid.errors.full_messages[0]
+  end
+
+  test 'invalid file id' do
+    assert_not @samples_workflow_executions_invalid_file_id.valid?
+    assert_not_nil @samples_workflow_executions_invalid_file_id.errors
+    expected_error = 'Attachment 12345 is not a valid IRIDA Next ID.'
+    assert_equal(
+      expected_error,
+      @samples_workflow_executions_invalid_file_id.errors.full_messages[0]
+    )
   end
 
-  test 'invalid no workflow execution' do
-    assert_not @samples_workflow_executions_invalid_no_workflow_execution.valid?
-    assert_not_nil @samples_workflow_executions_invalid_no_workflow_execution.errors
+  test 'mismatch file id' do
+    assert_not @samples_workflow_executions_mismatch_file_id.valid?
+    assert_not_nil @samples_workflow_executions_mismatch_file_id.errors
+    expected_error = 'Attachment Attachment does not belong to Sample INXT_SAM_AAAAAAAAAA.'
     assert_equal(
-      ['Workflow execution must exist'],
-      @samples_workflow_executions_invalid_no_workflow_execution.errors.full_messages
+      expected_error,
+      @samples_workflow_executions_mismatch_file_id.errors.full_messages[0]
     )
   end
 end
diff --git a/test/services/workflow_executions/create_service_test.rb b/test/services/workflow_executions/create_service_test.rb
index a6c9eefa2e..935a2c68c1 100644
--- a/test/services/workflow_executions/create_service_test.rb
+++ b/test/services/workflow_executions/create_service_test.rb
@@ -9,6 +9,15 @@ class CreateServiceTest < ActiveStorageTestCase
     def setup
       @user = users(:john_doe)
       @project = projects(:project1)
+      @sample = samples(:sample1)
+      @samples_workflow_executions_attributes = {
+        '0': {
+          sample_id: @sample.id,
+          samplesheet_params: {
+            sample: @sample.puid
+          }
+        }
+      }
     end
 
     test 'test create new workflow execution' do
@@ -27,7 +36,8 @@ def setup
         workflow_engine_parameters: { '-r': 'dev' },
         workflow_url: 'https://github.com/phac-nml/iridanextexamplenew',
         submitter_id: @user.id,
-        namespace_id: @project.namespace.id
+        namespace_id: @project.namespace.id,
+        samples_workflow_executions_attributes: @samples_workflow_executions_attributes
       }
 
       workflow_params2 = {
@@ -45,7 +55,8 @@ def setup
         workflow_engine_parameters: { '-r': 'dev' },
         workflow_url: 'https://github.com/phac-nml/iridanextexamplenew2',
         submitter_id: @user.id,
-        namespace_id: @project.namespace.id
+        namespace_id: @project.namespace.id,
+        samples_workflow_executions_attributes: @samples_workflow_executions_attributes
       }
 
       stub_request(:post, 'http://www.example.com/ga4gh/wes/v1/runs')
@@ -137,7 +148,8 @@ def setup
         workflow_engine_parameters: { '-r': 'dev' },
         workflow_url: 'https://github.com/phac-nml/iridanextexamplenew',
         submitter_id: @user.id,
-        namespace_id: @project.namespace.id
+        namespace_id: @project.namespace.id,
+        samples_workflow_executions_attributes: @samples_workflow_executions_attributes
       }
 
       @workflow_execution = WorkflowExecutions::CreateService.new(@user, workflow_params).execute
@@ -164,7 +176,8 @@ def setup
         workflow_engine_parameters: { '-r': 'dev' },
         workflow_url: 'https://github.com/phac-nml/iridanextexamplenew',
         submitter_id: @user.id,
-        namespace_id: @project.namespace.id
+        namespace_id: @project.namespace.id,
+        samples_workflow_executions_attributes: @samples_workflow_executions_attributes
       }
 
       @workflow_execution = WorkflowExecutions::CreateService.new(@user, workflow_params).execute
@@ -190,7 +203,8 @@ def setup
         workflow_engine_parameters: { '-r': 'dev' },
         workflow_url: 'https://github.com/phac-nml/iridanextexamplenew',
         submitter_id: @user.id,
-        namespace_id: @project.namespace.id
+        namespace_id: @project.namespace.id,
+        samples_workflow_executions_attributes: @samples_workflow_executions_attributes
       }
 
       stub_request(:post, 'http://www.example.com/ga4gh/wes/v1/runs').to_return(body: '{ "run_id": "create_run_4" }',
@@ -231,7 +245,8 @@ def setup
         workflow_engine_parameters: { '-r': 'dev' },
         workflow_url: 'https://github.com/phac-nml/iridanextexamplenew',
         submitter_id: @user.id,
-        namespace_id: @project.namespace.id
+        namespace_id: @project.namespace.id,
+        samples_workflow_executions_attributes: @samples_workflow_executions_attributes
       }
 
       stub_request(:post, 'http://www.example.com/ga4gh/wes/v1/runs').to_return(body: '{ "run_id": "create_run_5" }',
@@ -274,7 +289,8 @@ def setup
         workflow_engine_parameters: { engine: 'nextflow', execute_loc: 'azure' },
         workflow_url: 'https://github.com/phac-nml/iridanextexample',
         submitter_id: @user.id,
-        namespace_id: @project.namespace.id
+        namespace_id: @project.namespace.id,
+        samples_workflow_executions_attributes: @samples_workflow_executions_attributes
       }
 
       @workflow_execution = WorkflowExecutions::CreateService.new(@user, workflow_params).execute
@@ -305,7 +321,8 @@ def setup
         workflow_url: 'https://github.com/phac-nml/iridanextexamplenew',
         submitter_id: @user.id,
         namespace_id: @project.namespace.id,
-        name: test_name
+        name: test_name,
+        samples_workflow_executions_attributes: @samples_workflow_executions_attributes
       }
 
       @workflow_execution = WorkflowExecutions::CreateService.new(@user, workflow_params).execute
@@ -340,7 +357,8 @@ def setup
         workflow_engine_version: '23.10.0',
         workflow_engine_parameters: { '-r': 'dev' },
         workflow_url: 'https://github.com/phac-nml/iridanextexamplenew',
-        submitter_id: user.id
+        submitter_id: user.id,
+        samples_workflow_executions_attributes: @samples_workflow_executions_attributes
       }
 
       exception = assert_raises(ActionPolicy::Unauthorized) do
@@ -353,5 +371,78 @@ def setup
       assert_equal I18n.t(:'action_policy.policy.namespaces/project_namespace.submit_workflow?', name: @project.name),
                    exception.result.message
     end
+
+    test 'create new workflow execution with non matching sample puid in sample sheet' do
+      samples_workflow_executions_attributes = {
+        '0': {
+          sample_id: samples(:sample1).id,
+          samplesheet_params: {
+            sample: samples(:sample2).puid
+          }
+        }
+      }
+
+      workflow_params = {
+        metadata:
+          { workflow_name: 'phac-nml/iridanextexample', workflow_version: '1.0.2' },
+        workflow_params:
+        {
+          input: '/blah/samplesheet.csv',
+          outdir: '/blah/output'
+        },
+        workflow_type: 'NFL',
+        workflow_type_version: 'DSL2',
+        workflow_engine: 'nextflow',
+        workflow_engine_version: '23.10.0',
+        workflow_engine_parameters: { '-r': 'dev' },
+        workflow_url: 'https://github.com/phac-nml/iridanextexamplenew',
+        submitter_id: @user.id,
+        namespace_id: @project.namespace.id,
+        samples_workflow_executions_attributes: samples_workflow_executions_attributes
+      }
+
+      @workflow_execution = WorkflowExecutions::CreateService.new(@user, workflow_params).execute
+
+      assert @workflow_execution.errors.full_messages
+                                .include?('Sample Provided Sample PUID INXT_SAM_AAAAAAAAAB does not match SampleWorkflowExecution Sample PUID INXT_SAM_AAAAAAAAAA') # rubocop:disable Layout/LineLength
+      assert_enqueued_jobs(0, except: Turbo::Streams::BroadcastStreamJob)
+    end
+
+    test 'create new workflow execution with non matching attachments to sample' do
+      samples_workflow_executions_attributes = {
+        '0': {
+          sample_id: samples(:sample2).id,
+          samplesheet_params: {
+            sample: samples(:sample2).puid,
+            fastq_1: attachments(:attachment1).to_global_id # belongs to :sample1 # rubocop:disable Naming/VariableNumber
+          }
+        }
+      }
+
+      workflow_params = {
+        metadata:
+          { workflow_name: 'phac-nml/iridanextexample', workflow_version: '1.0.2' },
+        workflow_params:
+        {
+          input: '/blah/samplesheet.csv',
+          outdir: '/blah/output'
+        },
+        workflow_type: 'NFL',
+        workflow_type_version: 'DSL2',
+        workflow_engine: 'nextflow',
+        workflow_engine_version: '23.10.0',
+        workflow_engine_parameters: { '-r': 'dev' },
+        workflow_url: 'https://github.com/phac-nml/iridanextexamplenew',
+        submitter_id: @user.id,
+        namespace_id: @project.namespace.id,
+        samples_workflow_executions_attributes: samples_workflow_executions_attributes
+      }
+
+      @workflow_execution = WorkflowExecutions::CreateService.new(@user, workflow_params).execute
+
+      assert @workflow_execution.errors.full_messages
+                                .include?('Attachment Attachment does not belong to Sample INXT_SAM_AAAAAAAAAB.')
+      assert_enqueued_jobs(0, except: Turbo::Streams::BroadcastStreamJob)
+    end
   end
 end