Threat Model Analysis for nextflow-io/nextflow

Threat: Malicious Workflow Injection

Threat: Malicious Workflow Injection
- Description: An attacker submits a crafted Nextflow workflow (.nf file or a Git repository containing one) that contains malicious code. This code is executed by Nextflow as part of the workflow definition. The attacker might exploit a vulnerability in how Nextflow receives and processes workflow definitions (e.g., a web interface, API, or even a shared filesystem if Nextflow is configured to monitor it). The malicious code could be within the process blocks, in helper functions, or even in how channels are used.
- Impact:
  - Data Exfiltration: Sensitive data processed by the workflow could be stolen.
  - System Compromise: The attacker could gain control of the compute infrastructure where the workflow is executed via Nextflow's execution context.
  - Resource Abuse: The attacker could use the compute resources for malicious purposes.
  - Data Corruption: The attacker could modify or delete data.
  - Reputation Damage: Successful exploitation could damage reputation.
- Affected Nextflow Component:
  - Nextflow Engine (core execution logic, parsing and execution of .nf files).
  - Workflow Definition (.nf files) - This is the primary attack vector.
  - Process Definitions (within .nf files) - Where the malicious code resides.
  - Executor (indirectly, as it executes the code as directed by Nextflow).
- Risk Severity: Critical
- Mitigation Strategies:
  - Strict Input Validation: Implement rigorous validation of all workflow submissions, checking for malicious patterns, and limiting allowed commands before Nextflow parses them.
  - Code Review: Mandatory code review for all workflow definitions before they are allowed to run within the Nextflow environment.
  - Sandboxing: Execute workflows within isolated environments (containers, VMs) with limited privileges, managed by Nextflow's executor configuration.
  - Workflow Repository Control: Use a controlled repository (Git) with strict access controls and commit signing for all workflow definitions used by Nextflow.
  - Intrusion Detection: Monitor Nextflow's logs and system activity for suspicious behavior originating from workflow execution.

Threat: Configuration File Tampering (Targeting Nextflow)

Threat: Configuration File Tampering (Targeting Nextflow)
- Description: An attacker modifies the Nextflow configuration file (nextflow.config) to alter Nextflow's behavior. This is distinct from general system configuration tampering. The attacker targets settings specific to Nextflow, such as executor choices, resource limits, or security-related parameters (e.g., disabling signature verification). The attacker might gain access to the file through a compromised system or a misconfigured shared file system that Nextflow is configured to use.
- Impact:
  - Resource Exhaustion: The attacker could configure Nextflow to consume excessive resources.
  - Security Bypass: The attacker could disable Nextflow's security features or weaken security settings.
  - Data Leakage: The attacker could redirect output or intermediate data to insecure locations via Nextflow's configuration.
  - Execution Hijacking: The attacker could change the executor to a malicious one through Nextflow's settings.
- Affected Nextflow Component:
  - nextflow.config file - The direct target.
  - Nextflow Engine (core execution logic) - Interprets and applies the configuration.
  - Executor configuration - Specifically, the settings within nextflow.config.
- Risk Severity: High
- Mitigation Strategies:
  - Access Control: Implement strict access controls on the nextflow.config file, allowing only authorized users to modify it.
  - File Integrity Monitoring: Use file integrity monitoring tools to detect unauthorized changes to this specific file.
  - Regular Audits: Regularly audit the nextflow.config file for suspicious settings related to Nextflow's operation.
  - Version Control: Store the nextflow.config file in a version control system (Git) to track changes.
  - Configuration Validation: Implement validation checks within Nextflow or a wrapper script to ensure settings are within acceptable ranges and don't violate security policies.

Threat: Sensitive Data Exposure in Nextflow Logs/Outputs

Threat: Sensitive Data Exposure in Nextflow Logs/Outputs
- Description: Sensitive data is inadvertently printed to standard output, standard error, or log files due to actions within the Nextflow workflow or Nextflow's handling of process output. This is a direct threat to how Nextflow manages and presents information. The workflow scripts or the tools they use, as executed by Nextflow, might not be properly configured to handle sensitive data.
- Impact:
  - Data Breach: Sensitive data could be exposed.
  - Compliance Violations: Exposure of PII or regulated data.
  - Reputation Damage: Data breaches can damage reputation.
- Affected Nextflow Component:
  - Process Definitions (within .nf files) - Where the scripts and commands that might leak data are defined.
  - Nextflow Logging (standard output, standard error, .nextflow.log) - Nextflow's own logging mechanisms.
  - Executor (indirectly, as it captures the output as managed by Nextflow).
- Risk Severity: High
- Mitigation Strategies:
  - Avoid Hardcoding Secrets: Never hardcode sensitive data in workflow scripts.
  - Use Environment Variables: Store sensitive data in environment variables and access them securely within the workflow using Nextflow's mechanisms for environment variable handling.
  - Secrets Management: Use a secrets management system, integrating it with Nextflow's execution context.
  - Log Redaction: Implement log redaction specifically for Nextflow's logs and output streams.
  - Code Review: Review workflow scripts and configurations to ensure sensitive data is not being printed.
  - Secure Output Handling: Configure Nextflow and the executor to store output files securely, using Nextflow's directives for output management.
  - Nextflow secret directive (if applicable, and ensure it's used correctly).