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Check Hisat2 Files Specifications

Process Details

  • Name: check_Hisat2_files
  • Process UUID: cDUgrUluijLpH2BHad5z0mRzjiYlZX
  • Process Group: Index

Overview

This process validates the availability and integrity of HISAT2 index files required for RNA-seq alignment. It performs a systematic check of the specified HISAT2 index path to ensure all necessary index components are present and accessible before proceeding with the alignment workflow. The process uses a pathChecker function to generate the appropriate command for HISAT2 alignment execution.

This process is implemented in Bash, which utilizes internal validation functions for file system checks.

Key Functionality

  • Index Validation: Verifies the presence and accessibility of HISAT2 index files at the specified path
  • Conditional Execution: Only runs when HISAT2 alignment is enabled in the workflow parameters
  • Command Generation: Produces the appropriate HISAT2 command based on index availability and configuration
  • Path Resolution: Handles both provided index paths and default index locations

Input/Output Specification

Inputs

Optional Inputs

  • HISAT2 Index
    • Description: Pre-built HISAT2 index files for reference genome alignment
    • Format: Index directory containing HISAT2 index files

Outputs

  • HISAT2 Index
    • Description: Validated HISAT2 index files ready for alignment process
    • Format: Index directory with verified HISAT2 index components

References & Resources

  • Tool Documentation: Contact the team for details on the pathChecker validation function
  • Related Papers: Kim, D., Langmead, B. & Salzberg, S.L. HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12, 357–360 (2015). https://doi.org/10.1038/nmeth.3317