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Check Salmon Files Specifications

Process Details

  • Name: check_Salmon_files
  • Process UUID: RfFWoOoOiqzX2QCDP7kIGQbY39PKji
  • Process Group: Index

Overview

This process validates the presence and accessibility of Salmon index files in a specified input directory. It serves as a quality control step to ensure that required Salmon indexing files are available before proceeding with RNA-seq quantification workflows.

This process is implemented in Bash, which performs file system validation using a custom path checking function.

Key Functionality

  • File Validation: Verifies that Salmon index files exist in the specified directory
  • Path Checking: Uses a pathChecker function to validate folder accessibility and structure
  • Conditional Execution: Runs only when Salmon quantification is enabled in the workflow
  • Error Prevention: Prevents downstream failures by catching missing index files early

Input/Output Specification

Inputs

Optional Inputs

  • salmon_index
    • Description: Directory containing pre-built Salmon index files for transcript quantification
    • Format: folder

Outputs

  • salmon_index
    • Description: Validated Salmon index directory that has been confirmed to contain the necessary index files
    • Format: folder

Parameters & Settings

This process does not expose user-configurable parameters in the Foundry UI. It operates based on workflow-level settings that determine when Salmon quantification should be performed.

References & Resources

  • Tool Documentation: Contact the team for details on the pathChecker validation function