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Check Kallisto Files Specifications

Process Details

  • Name: check_kallisto_files
  • Process UUID: x1NbIRsFwXc0DmM1wdhK0YlNOt4QK7
  • Process Group: Index

Overview

This process validates the availability and integrity of Kallisto index files within their designated storage locations. It performs a systematic check to ensure that required Kallisto index files can be located and accessed before proceeding with downstream RNA-seq quantification workflows.

This process is implemented in Bash, which utilizes a path validation utility function for file system verification.

Key Functionality

  • Index File Validation: Verifies the presence and accessibility of Kallisto index files in their expected locations
  • Path Resolution: Resolves file paths and confirms proper file system permissions for index access
  • Workflow Gating: Acts as a quality control checkpoint before Kallisto quantification processes
  • Conditional Execution: Runs automatically when Kallisto quantification is enabled in the workflow

Input/Output Specification

Inputs

Optional Inputs

  • Kallisto Index
    • Description: Pre-built Kallisto index file for transcript quantification
    • Format: .idx file

Outputs

  • Kallisto Index
    • Description: Validated Kallisto index file confirmed to be accessible for downstream quantification
    • Format: .idx file

References & Resources

  • Tool Documentation: Contact the team for details on the path validation utility functions