diff --git a/.gitignore b/.gitignore
index 8d108886..90749d19 100644
--- a/.gitignore
+++ b/.gitignore
@@ -36,3 +36,6 @@ tests/logs/*
 tests/datafiles/*.tfvars
 tests/datafiles/secrets/*.json
 tests/.templatefile_cache
+
+# Generated files from modules
+**/generated/
diff --git a/modules/seqerakit/README.md b/modules/seqerakit/README.md
new file mode 100644
index 00000000..f6163da6
--- /dev/null
+++ b/modules/seqerakit/README.md
@@ -0,0 +1,195 @@
+# Seqerakit Module
+
+Generates and manages Seqerakit configuration files and scripts for Tower/Seqera Platform integration.
+
+## Features
+
+- Generates Seqerakit setup YAML configuration
+- Creates AWS Batch compute environment configurations  
+- Manages secrets loading from AWS Systems Manager (SSM)
+- Supports both Fusion v2 and traditional compute environments
+- Handles multiple credential types (AWS, GitHub, Docker, CodeCommit)
+- Generates CodeCommit workspace ID scripts
+
+## Usage
+
+```hcl
+module "seqerakit" {
+  source = "./modules/seqerakit/v1.0.0"
+
+  # Required Configuration
+  aws_account = var.aws_account
+  aws_region  = var.aws_region
+  aws_profile = var.aws_profile
+  default_tags = var.default_tags
+  app_name = var.app_name
+
+  # Seqerakit Settings
+  flag_run_seqerakit = true
+  seqerakit_org_name = "my-org"
+  seqerakit_org_fullname = "My Organization"
+  seqerakit_org_url = "https://my-org.seqera.io"
+  seqerakit_team_name = "my-team"
+  seqerakit_team_members = "user1@example.com,user2@example.com"
+  seqerakit_workspace_name = "my-workspace"
+  seqerakit_workspace_fullname = "My Workspace"
+  seqerakit_compute_env_name = "my-compute-env"
+  seqerakit_compute_env_region = "us-west-2"
+  seqerakit_root_bucket = "my-s3-bucket"
+  seqerakit_workdir = "/tmp/work"
+  seqerakit_outdir = "/tmp/output"
+
+  # AWS Configuration
+  seqerakit_aws_use_fusion_v2 = true
+  seqerakit_aws_use_forge = true
+  seqerakit_aws_use_batch = true
+  seqerakit_aws_fusion_instances = "m5.large,m5.xlarge"
+  seqerakit_aws_normal_instances = "t3.medium,t3.large"
+  seqerakit_aws_manual_head_queue = "head-queue"
+  seqerakit_aws_manual_compute_queue = "compute-queue"
+
+  # Credentials Configuration
+  seqerakit_flag_credential_create_aws = true
+  seqerakit_flag_credential_create_github = true
+  seqerakit_flag_credential_create_docker = true
+  seqerakit_flag_credential_create_codecommit = true
+  seqerakit_flag_credential_use_aws_role = false
+
+  # Infrastructure (optional)
+  vpc_id = var.vpc_id
+  subnet_ids = var.subnet_ids
+  security_group_ids = var.security_group_ids
+  ec2_key_pair_name = var.ec2_key_pair_name
+
+  # Secrets
+  secrets_bootstrap_seqerakit = "/myapp/seqerakit/secrets"
+}
+```
+
+## Secrets Management
+
+### Environment Variable Approach
+The module uses environment variables instead of hardcoded secrets for security:
+
+```bash
+# Load secrets from SSM into environment variables
+source helpers/load_seqerakit_secrets.sh
+
+# Run terraform to generate config files
+terraform apply
+```
+
+### SSM Parameter Structure
+Store secrets in SSM as a JSON object:
+
+```json
+{
+  "TOWER_AWS_USER": {"value": "AKIA..."},
+  "TOWER_AWS_PASSWORD": {"value": "secret..."},
+  "TOWER_AWS_ROLE": {"value": "arn:aws:iam::..."},
+  "TOWER_GITHUB_USER": {"value": "username"},
+  "TOWER_GITHUB_TOKEN": {"value": "ghp_..."},
+  "TOWER_DOCKER_USER": {"value": "username"},
+  "TOWER_DOCKER_TOKEN": {"value": "token..."},
+  "TOWER_CODECOMMIT_USER": {"value": "username"},
+  "TOWER_CODECOMMIT_PASSWORD": {"value": "password..."},
+  "TOWER_CODECOMMIT_REGION": {"value": "us-west-2"}
+}
+```
+
+### Loading Scripts
+```bash
+# Auto-detect AWS profile from terraform.tfvars
+source helpers/load_seqerakit_secrets.sh
+
+# Specify bootstrap path
+source helpers/load_seqerakit_secrets.sh /myapp/seqerakit/config
+
+# Specify both path and profile
+source helpers/load_seqerakit_secrets.sh /myapp/seqerakit/config playground
+```
+
+## Generated Files
+
+| File | Description |
+|------|-------------|
+| `setup.yml` | Main Seqerakit configuration |
+| `aws_batch_manual.yml` | AWS Batch compute environment |
+| `codecommit_set_workspace_id.sh` | CodeCommit workspace setup |
+| `load_seqerakit_secrets.sh` | Secrets loading script |
+
+## Inputs
+
+| Name | Description | Type | Default | Required |
+|------|-------------|------|---------|:--------:|
+| `aws_account` | AWS account ID | `string` | n/a | yes |
+| `aws_region` | AWS region | `string` | n/a | yes |
+| `aws_profile` | AWS profile to use | `string` | n/a | yes |
+| `default_tags` | Default tags to apply to all resources | `map(string)` | n/a | yes |
+| `app_name` | Application name | `string` | n/a | yes |
+| `flag_run_seqerakit` | Whether to run Seqerakit setup | `bool` | n/a | yes |
+| `seqerakit_org_name` | Seqerakit organization name | `string` | n/a | yes |
+| `seqerakit_org_fullname` | Seqerakit organization full name | `string` | n/a | yes |
+| `seqerakit_org_url` | Seqerakit organization URL | `string` | n/a | yes |
+| `seqerakit_team_name` | Seqerakit team name | `string` | n/a | yes |
+| `seqerakit_team_members` | Seqerakit team members (comma-separated) | `string` | n/a | yes |
+| `seqerakit_workspace_name` | Seqerakit workspace name | `string` | n/a | yes |
+| `seqerakit_workspace_fullname` | Seqerakit workspace full name | `string` | n/a | yes |
+| `seqerakit_compute_env_name` | Seqerakit compute environment name | `string` | n/a | yes |
+| `seqerakit_compute_env_region` | Seqerakit compute environment region | `string` | n/a | yes |
+| `seqerakit_root_bucket` | Seqerakit root S3 bucket | `string` | n/a | yes |
+| `seqerakit_workdir` | Seqerakit working directory | `string` | n/a | yes |
+| `seqerakit_outdir` | Seqerakit output directory | `string` | n/a | yes |
+| `seqerakit_aws_use_fusion_v2` | Whether to use Fusion v2 for Seqerakit | `bool` | n/a | yes |
+| `seqerakit_aws_use_forge` | Whether to use Forge for Seqerakit | `bool` | n/a | yes |
+| `seqerakit_aws_use_batch` | Whether to use AWS Batch for Seqerakit | `bool` | n/a | yes |
+| `seqerakit_aws_fusion_instances` | Fusion instance types for Seqerakit | `string` | n/a | yes |
+| `seqerakit_aws_normal_instances` | Normal instance types for Seqerakit | `string` | n/a | yes |
+| `seqerakit_aws_manual_head_queue` | Manual head queue for Seqerakit | `string` | n/a | yes |
+| `seqerakit_aws_manual_compute_queue` | Manual compute queue for Seqerakit | `string` | n/a | yes |
+| `seqerakit_flag_credential_create_aws` | Whether to create AWS credentials for Seqerakit | `bool` | n/a | yes |
+| `seqerakit_flag_credential_create_github` | Whether to create GitHub credentials for Seqerakit | `bool` | n/a | yes |
+| `seqerakit_flag_credential_create_docker` | Whether to create Docker credentials for Seqerakit | `bool` | n/a | yes |
+| `seqerakit_flag_credential_create_codecommit` | Whether to create CodeCommit credentials for Seqerakit | `bool` | n/a | yes |
+| `seqerakit_flag_credential_use_aws_role` | Whether to use AWS role for Seqerakit credentials | `bool` | n/a | yes |
+| `vpc_id` | VPC ID for compute environment | `string` | `""` | no |
+| `subnet_ids` | Subnet IDs for compute environment | `list(string)` | `[]` | no |
+| `security_group_ids` | Security group IDs for compute environment | `list(string)` | `[]` | no |
+| `ec2_key_pair_name` | EC2 Key pair name for compute environment | `string` | `""` | no |
+| `secrets_bootstrap_seqerakit` | SSM SecureString parameter name for Seqerakit secrets | `string` | n/a | yes |
+
+## Outputs
+
+| Name | Description |
+|------|-------------|
+| `seqerakit_yml` | Generated seqerakit setup YAML content |
+| `aws_batch_manual` | Generated AWS Batch manual compute environment YAML |
+| `codecommit_script` | Generated CodeCommit workspace ID script |
+| `load_secrets_script` | Script to load Seqerakit secrets from SSM into environment variables |
+| `generated_files` | Map of generated file paths |
+| `seqerakit_secrets` | Seqerakit secrets from SSM (sensitive) |
+
+## Troubleshooting
+
+### Missing Environment Variables
+```bash
+# Check if secrets are loaded
+echo $TOWER_AWS_USER
+echo $TOWER_GITHUB_TOKEN
+
+# Verify SSM parameter exists
+aws ssm get-parameter --name "/myapp/seqerakit/secrets" --with-decryption
+```
+
+### Empty Values
+Empty values are normal if certain credentials aren't configured in your bootstrap parameter.
+
+## Requirements
+
+- Terraform >= 1.0
+- AWS Provider >= 5.0
+- Local Provider >= 2.0
+
+## Version History
+
+- **v1.0.0** - Initial release with consolidated module structure and environment variable secrets
\ No newline at end of file
diff --git a/modules/seqerakit/v1.0.0/compute-envs/aws_batch_manual.yml.tpl b/modules/seqerakit/v1.0.0/compute-envs/aws_batch_manual.yml.tpl
new file mode 100644
index 00000000..373c6b37
--- /dev/null
+++ b/modules/seqerakit/v1.0.0/compute-envs/aws_batch_manual.yml.tpl
@@ -0,0 +1,14 @@
+compute-envs:
+  - type: aws-batch 
+    config-mode: manual
+    name: "${seqerakit_compute_env_name}"
+    workspace: "${seqerakit_org_name}/${seqerakit_workspace_name}"
+    credentials: 'aws_credentials'
+    work-dir: ${seqerakit_workdir}
+    region: ${aws_region}
+    head-queue: ${seqerakit_aws_manual_head_queue}
+    compute-queue: ${seqerakit_aws_manual_compute_queue}
+    fusion-v2: ${use_fusion_v2}
+    wave: ${use_wave}
+    wait: 'AVAILABLE'
+    overwrite: True
\ No newline at end of file
diff --git a/modules/seqerakit/v1.0.0/credentials/codecommit.json b/modules/seqerakit/v1.0.0/credentials/codecommit.json
new file mode 100644
index 00000000..7c310427
--- /dev/null
+++ b/modules/seqerakit/v1.0.0/credentials/codecommit.json
@@ -0,0 +1,13 @@
+{
+  "credentials": {
+    "name": "myCodeCommit",
+    "description": "myCodeCommit",
+    "provider": "codecommit",
+    "baseUrl": "WILL_BE_SUBSTITUTED_BY_ANSIBLE",
+    "category": "dunno",
+    "keys": {
+      "username": "WILL_BE_SUBSTITUTED_BY_ANSIBLE",
+      "password": "WILL_BE_SUBSTITUTED_BY_ANSIBLE"
+    }
+  }
+}
\ No newline at end of file
diff --git a/modules/seqerakit/v1.0.0/helpers/codecommit_set_workspace_id.sh.tpl b/modules/seqerakit/v1.0.0/helpers/codecommit_set_workspace_id.sh.tpl
new file mode 100644
index 00000000..37f247b8
--- /dev/null
+++ b/modules/seqerakit/v1.0.0/helpers/codecommit_set_workspace_id.sh.tpl
@@ -0,0 +1,5 @@
+#!/usr/bin/env sh
+
+# Add TF vars here and export to keep segregated.
+export CC_ORG_NAME=${seqerakit_org_name}
+export CC_WORKSPACE_NAME=${seqerakit_workspace_name}
\ No newline at end of file
diff --git a/modules/seqerakit/v1.0.0/helpers/load_seqerakit_secrets.sh b/modules/seqerakit/v1.0.0/helpers/load_seqerakit_secrets.sh
new file mode 100755
index 00000000..83a9e054
--- /dev/null
+++ b/modules/seqerakit/v1.0.0/helpers/load_seqerakit_secrets.sh
@@ -0,0 +1,75 @@
+#!/bin/bash
+
+# ------------------------------------------------------------------------------------
+# Load Seqerakit Secrets from SSM into Environment Variables
+# ------------------------------------------------------------------------------------
+# Usage: source load_seqerakit_secrets.sh [bootstrap_ssm_path] [aws_profile] [aws_region]
+# Example: source load_seqerakit_secrets.sh /scidev/seqerakit/config playground us-east-1
+# ------------------------------------------------------------------------------------
+
+# set -e
+
+# Get parameters
+BOOTSTRAP_SSM_PATH=${1:-"/scidev/seqerakit/config"}
+AWS_PROFILE_PARAM=${2:-"$AWS_PROFILE"}
+AWS_REGION_PARAM=${3:-"$AWS_DEFAULT_REGION"}
+
+echo "Loading secrets from: $BOOTSTRAP_SSM_PATH"
+if [ -n "$AWS_PROFILE_PARAM" ]; then
+    echo "Using AWS profile: $AWS_PROFILE_PARAM"
+    export AWS_PROFILE="$AWS_PROFILE_PARAM"
+fi
+if [ -n "$AWS_REGION_PARAM" ]; then
+    echo "Using AWS region: $AWS_REGION_PARAM"
+    export AWS_DEFAULT_REGION="$AWS_REGION_PARAM"
+    export AWS_REGION="$AWS_REGION_PARAM"
+fi
+
+# Check dependencies
+if ! command -v jq &> /dev/null; then
+    echo "❌ Error: jq is required. Install with: brew install jq"
+    return 1
+fi
+
+if ! command -v aws &> /dev/null; then
+    echo "❌ Error: AWS CLI is required"
+    return 1
+fi
+
+# Test AWS CLI
+if ! aws sts get-caller-identity &>/dev/null; then
+    echo "❌ Error: AWS CLI not configured. Run 'aws configure' or 'aws sso login'"
+    return 1
+fi
+
+# Get the bootstrap parameter
+BOOTSTRAP_JSON=$(aws ssm get-parameters \
+    --name "$BOOTSTRAP_SSM_PATH" \
+    --with-decryption \
+    --query "Parameters[*].{Value:Value}" \
+    --output text)
+
+if [ -z "$BOOTSTRAP_JSON" ] || [ "$BOOTSTRAP_JSON" = "None" ]; then
+    echo "❌ Error: Parameter not found: $BOOTSTRAP_SSM_PATH"
+    return 1
+fi
+
+# Validate JSON
+if ! echo "$BOOTSTRAP_JSON" | jq empty 2>/dev/null; then
+    echo "❌ Error: Invalid JSON in parameter"
+    return 1
+fi
+
+# Extract and set environment variables
+export TOWER_AWS_USER=$(echo "$BOOTSTRAP_JSON" | jq -r '.["TOWER_AWS_USER"]["value"] // empty')
+export TOWER_AWS_PASSWORD=$(echo "$BOOTSTRAP_JSON" | jq -r '.["TOWER_AWS_PASSWORD"]["value"] // empty')
+export TOWER_AWS_ROLE=$(echo "$BOOTSTRAP_JSON" | jq -r '.["TOWER_AWS_ROLE"]["value"] // empty')
+export TOWER_GITHUB_USER=$(echo "$BOOTSTRAP_JSON" | jq -r '.["TOWER_GITHUB_USER"]["value"] // empty')
+export TOWER_GITHUB_TOKEN=$(echo "$BOOTSTRAP_JSON" | jq -r '.["TOWER_GITHUB_TOKEN"]["value"] // empty')
+export TOWER_DOCKER_USER=$(echo "$BOOTSTRAP_JSON" | jq -r '.["TOWER_DOCKER_USER"]["value"] // empty')
+export TOWER_DOCKER_TOKEN=$(echo "$BOOTSTRAP_JSON" | jq -r '.["TOWER_DOCKER_TOKEN"]["value"] // empty')
+export TOWER_CODECOMMIT_USER=$(echo "$BOOTSTRAP_JSON" | jq -r '.["TOWER_CODECOMMIT_USER"]["value"] // empty')
+export TOWER_CODECOMMIT_PASSWORD=$(echo "$BOOTSTRAP_JSON" | jq -r '.["TOWER_CODECOMMIT_PASSWORD"]["value"] // empty')
+export TOWER_CODECOMMIT_REGION=$(echo "$BOOTSTRAP_JSON" | jq -r '.["TOWER_CODECOMMIT_REGION"]["value"] // empty')
+
+echo "✓ Secrets loaded successfully"
diff --git a/modules/seqerakit/v1.0.0/helpers/split_for_codecommit.py b/modules/seqerakit/v1.0.0/helpers/split_for_codecommit.py
new file mode 100644
index 00000000..6237388f
--- /dev/null
+++ b/modules/seqerakit/v1.0.0/helpers/split_for_codecommit.py
@@ -0,0 +1,29 @@
+#!/usr/bin/env python3
+import yaml
+
+yaml.sort_base_mapping_type_on_output = False
+
+original_setup = open('../setup.yml', 'r')
+
+cc_first_keys = ["organizations","workspaces","teams","participants","credentials"]
+cc_second_keys = ["pipelines","launch","compute-envs"]
+
+cc_first_dict = {}
+cc_second_dict = {}
+
+original_yaml = yaml.safe_load(original_setup) #, Loader=Loader)
+
+
+for key in cc_first_keys:
+    cc_first_dict[key] = original_yaml[key]
+
+for key in cc_second_keys:
+    cc_second_dict[key] = original_yaml[key]
+
+
+with open('../cc_first.yaml', 'w') as yamlfile:
+    yaml.safe_dump(cc_first_dict, yamlfile, sort_keys=False)
+
+with open('../cc_second.yaml', 'w') as yamlfile:
+    yaml.safe_dump(cc_second_dict, yamlfile, sort_keys=False)
+
diff --git a/modules/seqerakit/v1.0.0/main.tf b/modules/seqerakit/v1.0.0/main.tf
new file mode 100644
index 00000000..7da9819e
--- /dev/null
+++ b/modules/seqerakit/v1.0.0/main.tf
@@ -0,0 +1,143 @@
+## ------------------------------------------------------------------------------------
+## Seqerakit Module - Main Configuration
+## ------------------------------------------------------------------------------------
+
+## ------------------------------------------------------------------------------------
+## Data Sources
+## ------------------------------------------------------------------------------------
+data "aws_ssm_parameter" "seqerakit_secrets" {
+  count = var.secrets_bootstrap_seqerakit != "" ? 1 : 0
+  name  = var.secrets_bootstrap_seqerakit
+}
+
+## ------------------------------------------------------------------------------------
+## Locals
+## ------------------------------------------------------------------------------------
+locals {
+  # Use SSM secrets if available, otherwise use empty values
+  seqerakit_secrets = var.secrets_bootstrap_seqerakit != "" ? jsondecode(nonsensitive(data.aws_ssm_parameter.seqerakit_secrets[0].value)) : {
+    "TOWER_AWS_USER" = { "value" = "CHANGE_ME" }
+    "TOWER_AWS_PASSWORD" = { "value" = "CHANGE_ME" }
+    "TOWER_AWS_ROLE" = { "value" = "CHANGE_ME" }
+    "TOWER_GITHUB_USER" = { "value" = "CHANGE_ME" }
+    "TOWER_GITHUB_TOKEN" = { "value" = "CHANGE_ME" }
+    "TOWER_DOCKER_USER" = { "value" = "CHANGE_ME" }
+    "TOWER_DOCKER_TOKEN" = { "value" = "CHANGE_ME" }
+    "TOWER_CODECOMMIT_USER" = { "value" = "CHANGE_ME" }
+    "TOWER_CODECOMMIT_PASSWORD" = { "value" = "CHANGE_ME" }
+    "TOWER_CODECOMMIT_REGION" = { "value" = "CHANGE_ME" }
+  }
+
+  # Seqerakit - Main Configuration Template
+  seqerakit_yml = templatefile("${path.module}/setup.yml.tpl",
+    {
+      seqerakit_org_name     = var.seqerakit_org_name,
+      seqerakit_org_fullname = var.seqerakit_org_fullname,
+      seqerakit_org_url      = var.seqerakit_org_url,
+
+      seqerakit_team_name    = var.seqerakit_team_name,
+      seqerakit_team_members = replace(var.seqerakit_team_members, "/\\s+/", ""),
+
+      seqerakit_workspace_name     = var.seqerakit_workspace_name,
+      seqerakit_workspace_fullname = var.seqerakit_workspace_fullname,
+
+      seqerakit_workdir          = var.seqerakit_workdir,
+      seqerakit_outdir           = var.seqerakit_outdir,
+      seqerakit_compute_env_name = var.seqerakit_compute_env_name,
+
+      seqerakit_flag_credential_create_aws    = var.seqerakit_flag_credential_create_aws,
+      seqerakit_flag_credential_create_github = var.seqerakit_flag_credential_create_github,
+      seqerakit_flag_credential_create_docker = var.seqerakit_flag_credential_create_docker,
+      seqerakit_flag_credential_create_codecommit = var.seqerakit_flag_credential_create_codecommit,
+
+      seqerakit_flag_credential_use_aws_role = var.seqerakit_flag_credential_use_aws_role
+
+      # Environment variable names for secrets (values sourced from SSM)
+      aws_access_key_env_var = "$TOWER_AWS_USER"
+      aws_secret_key_env_var = "$TOWER_AWS_PASSWORD"
+      aws_role_arn_env_var   = "$TOWER_AWS_ROLE"
+      github_username_env_var = "$TOWER_GITHUB_USER"
+      github_token_env_var   = "$TOWER_GITHUB_TOKEN"
+      docker_username_env_var = "$TOWER_DOCKER_USER"
+      docker_password_env_var = "$TOWER_DOCKER_TOKEN"
+
+      # Compute environment variables
+      seqerakit_aws_use_forge = var.seqerakit_aws_use_forge,
+      aws_region = var.seqerakit_compute_env_region,
+      vpc_id = var.vpc_id,
+      subnets = length(var.subnet_ids) > 0 ? join(",", var.subnet_ids) : "",
+      securityGroups = length(var.security_group_ids) > 0 ? join(",", var.security_group_ids) : "",
+      ec2KeyPair = var.ec2_key_pair_name,
+
+      use_fusion_v2    = var.seqerakit_aws_use_fusion_v2 == true ? "True" : "False",
+      use_wave         = var.seqerakit_aws_use_fusion_v2 == true ? "True" : "False",
+      use_fast_storage = var.seqerakit_aws_use_fusion_v2 == true ? "True" : "False",
+
+      instance_types = (
+        var.seqerakit_aws_use_fusion_v2 == true ?
+        replace(var.seqerakit_aws_fusion_instances, "/\\s+/", "") :
+        replace(var.seqerakit_aws_normal_instances, "/\\s+/", "")
+      )
+    }
+  )
+
+  # Seqerakit - AWS Batch Manual Compute Environment Template
+  aws_batch_manual = templatefile("${path.module}/compute-envs/aws_batch_manual.yml.tpl",
+    {
+      aws_region = var.seqerakit_compute_env_region,
+
+      seqerakit_org_name         = var.seqerakit_org_name,
+      seqerakit_workspace_name   = var.seqerakit_workspace_name,
+      seqerakit_workdir          = var.seqerakit_workdir,
+      seqerakit_compute_env_name = var.seqerakit_compute_env_name,
+
+      seqerakit_aws_manual_head_queue    = var.seqerakit_aws_manual_head_queue,
+      seqerakit_aws_manual_compute_queue = var.seqerakit_aws_manual_compute_queue,
+
+      use_fusion_v2    = var.seqerakit_aws_use_fusion_v2 == true ? "True" : "False",
+      use_wave         = var.seqerakit_aws_use_fusion_v2 == true ? "True" : "False",
+      use_fast_storage = var.seqerakit_aws_use_fusion_v2 == true ? "True" : "False"
+    }
+  )
+
+  # Seqerakit - CodeCommit Workspace ID Script Template
+  codecommit_seqerakit = templatefile("${path.module}/helpers/codecommit_set_workspace_id.sh.tpl",
+    {
+      seqerakit_org_name = var.seqerakit_org_name,
+      seqerakit_workspace_name = var.seqerakit_workspace_name
+    }
+  )
+}
+
+## ------------------------------------------------------------------------------------
+## Resources
+## ------------------------------------------------------------------------------------
+resource "local_file" "seqerakit_yml" {
+  content  = local.seqerakit_yml
+  filename = "${path.module}/generated/setup.yml"
+}
+
+resource "local_file" "aws_batch_manual_yml" {
+  content  = local.aws_batch_manual
+  filename = "${path.module}/generated/aws_batch_manual.yml"
+}
+
+resource "local_file" "codecommit_script" {
+  content  = local.codecommit_seqerakit
+  filename = "${path.module}/generated/codecommit_set_workspace_id.sh"
+}
+
+# Copy the secrets loading script
+resource "local_file" "load_secrets_script" {
+  source   = "${path.module}/helpers/load_seqerakit_secrets.sh"
+  filename = "${path.module}/generated/load_seqerakit_secrets.sh"
+}
+
+# Make scripts executable
+resource "null_resource" "make_scripts_executable" {
+  depends_on = [local_file.codecommit_script, local_file.load_secrets_script]
+  
+  provisioner "local-exec" {
+    command = "chmod +x ${path.module}/generated/codecommit_set_workspace_id.sh ${path.module}/generated/load_seqerakit_secrets.sh"
+  }
+}
diff --git a/modules/seqerakit/v1.0.0/outputs.tf b/modules/seqerakit/v1.0.0/outputs.tf
new file mode 100644
index 00000000..c9acd820
--- /dev/null
+++ b/modules/seqerakit/v1.0.0/outputs.tf
@@ -0,0 +1,44 @@
+## ------------------------------------------------------------------------------------
+## Seqerakit Configuration Outputs
+## ------------------------------------------------------------------------------------
+output "seqerakit_yml" {
+  description = "Generated seqerakit setup YAML content"
+  value       = local.seqerakit_yml
+}
+
+output "aws_batch_manual" {
+  description = "Generated AWS Batch manual compute environment YAML"
+  value       = local.aws_batch_manual
+}
+
+output "codecommit_script" {
+  description = "Generated CodeCommit workspace ID script"
+  value       = local.codecommit_seqerakit
+}
+
+output "load_secrets_script" {
+  description = "Script to load Seqerakit secrets from SSM into environment variables"
+  value       = "${path.module}/generated/load_seqerakit_secrets.sh"
+}
+
+## ------------------------------------------------------------------------------------
+## Generated Files Outputs
+## ------------------------------------------------------------------------------------
+output "generated_files" {
+  description = "Map of generated file paths"
+  value = {
+    setup_yml                    = local_file.seqerakit_yml.filename
+    aws_batch_manual_yml         = local_file.aws_batch_manual_yml.filename
+    codecommit_script            = local_file.codecommit_script.filename
+    load_secrets_script          = local_file.load_secrets_script.filename
+  }
+}
+
+## ------------------------------------------------------------------------------------
+## Secrets Outputs
+## ------------------------------------------------------------------------------------
+output "seqerakit_secrets" {
+  description = "Seqerakit secrets from SSM (sensitive)"
+  value       = local.seqerakit_secrets
+  sensitive   = true
+}
diff --git a/modules/seqerakit/v1.0.0/pipelines/nextflow.config b/modules/seqerakit/v1.0.0/pipelines/nextflow.config
new file mode 100755
index 00000000..612d322a
--- /dev/null
+++ b/modules/seqerakit/v1.0.0/pipelines/nextflow.config
@@ -0,0 +1 @@
+process.maxRetries = 1
\ No newline at end of file
diff --git a/modules/seqerakit/v1.0.0/pipelines/post_run.txt b/modules/seqerakit/v1.0.0/pipelines/post_run.txt
new file mode 100644
index 00000000..b1d97ec0
--- /dev/null
+++ b/modules/seqerakit/v1.0.0/pipelines/post_run.txt
@@ -0,0 +1 @@
+echo "hello from post run!"
\ No newline at end of file
diff --git a/modules/seqerakit/v1.0.0/pipelines/pre_run.txt b/modules/seqerakit/v1.0.0/pipelines/pre_run.txt
new file mode 100755
index 00000000..e0747cf6
--- /dev/null
+++ b/modules/seqerakit/v1.0.0/pipelines/pre_run.txt
@@ -0,0 +1 @@
+export NXF_VER=24.04.2
\ No newline at end of file
diff --git a/modules/seqerakit/v1.0.0/setup.yml.tpl b/modules/seqerakit/v1.0.0/setup.yml.tpl
new file mode 100644
index 00000000..17ab1eae
--- /dev/null
+++ b/modules/seqerakit/v1.0.0/setup.yml.tpl
@@ -0,0 +1,156 @@
+organizations:
+  - name: "${seqerakit_org_name}"
+    full-name: "${seqerakit_org_fullname}"
+    description: "Description for ${seqerakit_org_name}"
+    location: 'Global'
+    website: "${seqerakit_org_url}"
+    overwrite: False
+
+workspaces:
+  - name: "${seqerakit_workspace_name}"
+    full-name: "${seqerakit_workspace_fullname}"
+    organization: "${seqerakit_org_name}"
+    description: 'Workspace for ${seqerakit_workspace_name}'
+    visibility: 'PRIVATE'
+    overwrite: False
+
+teams:
+  - name: "${seqerakit_team_name}"
+    organization: "${seqerakit_org_name}"
+    description: "Description for ${seqerakit_team_name}"
+    members: [ ${seqerakit_team_members } ]
+    overwrite: False
+
+participants:
+  - name: "${seqerakit_team_name}"
+    type: 'TEAM'
+    workspace: "${seqerakit_org_name}/${seqerakit_workspace_name}"
+    role: 'ADMIN'
+    overwrite: False
+
+credentials:
+%{~ if seqerakit_flag_credential_create_aws == true }
+  - type: 'aws'
+    name: 'aws_credentials'
+    workspace: "${seqerakit_org_name}/${seqerakit_workspace_name}"
+    access-key: ${aws_access_key_env_var}
+    secret-key: ${aws_secret_key_env_var}
+    %{~ if seqerakit_flag_credential_use_aws_role == true ~}
+    assume-role-arn: ${aws_role_arn_env_var}
+    %{~ endif ~}
+    overwrite: False
+%{ endif ~}
+
+%{~ if seqerakit_flag_credential_create_docker == true }
+  - type: 'container-reg'
+    name: 'dockerhub_credentials'
+    workspace: "${seqerakit_org_name}/${seqerakit_workspace_name}"
+    username: ${docker_username_env_var}
+    password: ${docker_password_env_var}
+    registry: 'docker.io'
+    overwrite: False
+%{ endif ~}
+
+%{~ if seqerakit_flag_credential_create_github == true }
+  - type: 'github'
+    name: 'github_credentials'
+    workspace: "${seqerakit_org_name}/${seqerakit_workspace_name}"
+    username: ${github_username_env_var}
+    password: ${github_token_env_var}
+    overwrite: False
+%{ endif ~}
+
+compute-envs:
+%{~ if seqerakit_aws_use_forge == true }
+  - type: aws-batch
+    config-mode: forge
+    name: "${seqerakit_compute_env_name}"
+    workspace: "${seqerakit_org_name}/${seqerakit_workspace_name}"
+    credentials: 'aws_credentials'
+    region: "${aws_region}"
+    work-dir: "${seqerakit_workdir}"
+    provisioning-model: SPOT
+    fusion-v2: ${use_fusion_v2}
+    wave: ${use_wave}
+    fargate: False
+    fast-storage: ${use_fast_storage}
+    instance-types: "${instance_types}"
+    no-ebs-auto-scale: True
+    max-cpus: 500
+    wait: AVAILABLE
+%{~ if vpc_id != "" ~}
+    vpc-id: "${vpc_id}"
+%{~ endif ~}
+%{~ if subnets != "" ~}
+    subnets: "${subnets}"
+%{~ endif ~}
+%{~ if securityGroups != "" ~}
+    security-groups: "${securityGroups}"
+%{~ endif ~}
+%{~ if ec2KeyPair != "" ~}
+    key-pair: "${ec2KeyPair}"
+%{~ endif ~}
+%{ endif ~}
+
+pipelines:
+  - name: 'hello-world'
+    url: 'https://github.com/nextflow-io/hello'
+    workspace: "${seqerakit_org_name}/${seqerakit_workspace_name}"
+    description: 'Tiny hello world pipeline composed of four tasks.'
+    compute-env: "${seqerakit_compute_env_name}"
+    work-dir: "${seqerakit_workdir}"
+    revision: 'master'
+    config: '../pipelines/nextflow.config'
+    pre-run: '../pipelines/pre_run.txt'
+    post-run: '../pipelines/post_run.txt'
+    overwrite: False
+
+  - name: 'nf-core-rnaseq-test'
+    url: 'https://github.com/nf-core/rnaseq'
+    workspace: "${seqerakit_org_name}/${seqerakit_workspace_name}"
+    description: 'RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.'
+    compute-env: "${seqerakit_compute_env_name}"
+    work-dir: "${seqerakit_workdir}"
+    profile: 'test'
+    labels: 'profile_test'
+    revision: '3.12.0'
+    params:
+      outdir: "${seqerakit_outdir}"
+    config: '../pipelines/nextflow.config'
+    pre-run: '../pipelines/pre_run.txt'
+    overwrite: False
+
+  - name: 'nf-core-rnaseq-test-full'
+    url: 'https://github.com/nf-core/rnaseq'
+    workspace: "${seqerakit_org_name}/${seqerakit_workspace_name}"
+    description: 'RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.'
+    compute-env: "${seqerakit_compute_env_name}"
+    work-dir: "${seqerakit_workdir}"
+    profile: 'test_full'
+    labels: 'profile_test_full'
+    revision: '3.12.0'
+    params:
+      outdir: "${seqerakit_outdir}"
+    config: '../pipelines/nextflow.config'
+    pre-run: '../pipelines/pre_run.txt'
+    overwrite: False
+
+%{~ if seqerakit_flag_credential_create_codecommit == true }
+  # CodeCommitTest
+  - name: 'cc-test'
+    url: 'https://git-codecommit.us-east-1.amazonaws.com/v1/repos/grahamhello'
+    workspace: "${seqerakit_org_name}/${seqerakit_workspace_name}"
+    description: 'CodeCommit testing pipeline'
+    compute-env: "${seqerakit_compute_env_name}"
+    work-dir: "${seqerakit_workdir}"
+    revision: 'main'
+    overwrite: False
+%{ endif ~}
+
+
+
+launch:
+  - name: 'hello-world-launchpad'
+    workspace: "${seqerakit_org_name}/${seqerakit_workspace_name}"
+    pipeline: 'hello-world'
+
diff --git a/modules/seqerakit/v1.0.0/variables.tf b/modules/seqerakit/v1.0.0/variables.tf
new file mode 100644
index 00000000..f821f041
--- /dev/null
+++ b/modules/seqerakit/v1.0.0/variables.tf
@@ -0,0 +1,202 @@
+## ------------------------------------------------------------------------------------
+## AWS Configuration
+## ------------------------------------------------------------------------------------
+variable "aws_account" {
+  description = "AWS account ID"
+  type        = string
+}
+
+variable "aws_region" {
+  description = "AWS region"
+  type        = string
+}
+
+variable "aws_profile" {
+  description = "AWS profile to use"
+  type        = string
+}
+
+## ------------------------------------------------------------------------------------
+## Tags
+## ------------------------------------------------------------------------------------
+variable "default_tags" {
+  description = "Default tags to apply to all resources"
+  type        = map(string)
+}
+
+## ------------------------------------------------------------------------------------
+## App Configuration
+## ------------------------------------------------------------------------------------
+variable "app_name" {
+  description = "Application name"
+  type        = string
+}
+
+## ------------------------------------------------------------------------------------
+## Seqerakit Configuration
+## ------------------------------------------------------------------------------------
+variable "flag_run_seqerakit" {
+  description = "Whether to run Seqerakit setup"
+  type        = bool
+}
+
+variable "seqerakit_org_name" {
+  description = "Seqerakit organization name"
+  type        = string
+}
+
+variable "seqerakit_org_fullname" {
+  description = "Seqerakit organization full name"
+  type        = string
+}
+
+variable "seqerakit_org_url" {
+  description = "Seqerakit organization URL"
+  type        = string
+}
+
+variable "seqerakit_team_name" {
+  description = "Seqerakit team name"
+  type        = string
+}
+
+variable "seqerakit_team_members" {
+  description = "Seqerakit team members (comma-separated)"
+  type        = string
+}
+
+variable "seqerakit_workspace_name" {
+  description = "Seqerakit workspace name"
+  type        = string
+}
+
+variable "seqerakit_workspace_fullname" {
+  description = "Seqerakit workspace full name"
+  type        = string
+}
+
+variable "seqerakit_compute_env_name" {
+  description = "Seqerakit compute environment name"
+  type        = string
+}
+
+variable "seqerakit_compute_env_region" {
+  description = "Seqerakit compute environment region"
+  type        = string
+}
+
+variable "seqerakit_root_bucket" {
+  description = "Seqerakit root S3 bucket"
+  type        = string
+}
+
+variable "seqerakit_workdir" {
+  description = "Seqerakit working directory"
+  type        = string
+}
+
+variable "seqerakit_outdir" {
+  description = "Seqerakit output directory"
+  type        = string
+}
+
+## ------------------------------------------------------------------------------------
+## Seqerakit AWS Configuration
+## ------------------------------------------------------------------------------------
+variable "seqerakit_aws_use_fusion_v2" {
+  description = "Whether to use Fusion v2 for Seqerakit"
+  type        = bool
+}
+
+variable "seqerakit_aws_use_forge" {
+  description = "Whether to use Forge for Seqerakit"
+  type        = bool
+}
+
+variable "seqerakit_aws_use_batch" {
+  description = "Whether to use AWS Batch for Seqerakit"
+  type        = bool
+}
+
+variable "seqerakit_aws_fusion_instances" {
+  description = "Fusion instance types for Seqerakit"
+  type        = string
+}
+
+variable "seqerakit_aws_normal_instances" {
+  description = "Normal instance types for Seqerakit"
+  type        = string
+}
+
+variable "seqerakit_aws_manual_head_queue" {
+  description = "Manual head queue for Seqerakit"
+  type        = string
+}
+
+variable "seqerakit_aws_manual_compute_queue" {
+  description = "Manual compute queue for Seqerakit"
+  type        = string
+}
+
+## ------------------------------------------------------------------------------------
+## Seqerakit Credentials Configuration
+## ------------------------------------------------------------------------------------
+variable "seqerakit_flag_credential_create_aws" {
+  description = "Whether to create AWS credentials for Seqerakit"
+  type        = bool
+}
+
+variable "seqerakit_flag_credential_create_github" {
+  description = "Whether to create GitHub credentials for Seqerakit"
+  type        = bool
+}
+
+variable "seqerakit_flag_credential_create_docker" {
+  description = "Whether to create Docker credentials for Seqerakit"
+  type        = bool
+}
+
+variable "seqerakit_flag_credential_create_codecommit" {
+  description = "Whether to create CodeCommit credentials for Seqerakit"
+  type        = bool
+}
+
+variable "seqerakit_flag_credential_use_aws_role" {
+  description = "Whether to use AWS role for Seqerakit credentials"
+  type        = bool
+}
+
+## ------------------------------------------------------------------------------------
+## Infrastructure Dependencies
+## ------------------------------------------------------------------------------------
+variable "vpc_id" {
+  description = "VPC ID for compute environment"
+  type        = string
+  default     = ""
+}
+
+variable "subnet_ids" {
+  description = "Subnet IDs for compute environment"
+  type        = list(string)
+  default     = []
+}
+
+variable "security_group_ids" {
+  description = "Security group IDs for compute environment"
+  type        = list(string)
+  default     = []
+}
+
+variable "ec2_key_pair_name" {
+  description = "EC2 Key pair name for compute environment"
+  type        = string
+  default     = ""
+}
+
+## ------------------------------------------------------------------------------------
+## Secrets Configuration
+## ------------------------------------------------------------------------------------
+variable "secrets_bootstrap_seqerakit" {
+  description = "SSM SecureString parameter name for Seqerakit secrets"
+  type        = string
+}