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Check Bowtie2 Files Specifications

Process Details

  • Name: check_Bowtie2_files
  • Process UUID: a1dxJlIiTp2IIjilm4G9mqpLNrNnq1
  • Process Group: Index

Overview

This process validates the availability and integrity of Bowtie2 index files within the specified index directory. It performs a systematic check to ensure that all required Bowtie2 index components are present and accessible before proceeding with downstream alignment processes.

This process is implemented in Bash.

Key Functionality

  • Index Validation: Verifies that Bowtie2 index files exist in the expected directory location
  • Path Resolution: Resolves and validates file paths for Bowtie2 index components
  • Conditional Execution: Runs automatically when Bowtie2 alignment is enabled in the pipeline configuration

Input/Output Specification

Inputs

Optional Inputs

  • bowtie2index
    • Description: Bowtie2 index directory containing pre-built index files for sequence alignment
    • Format: bowtie2index

Outputs

  • bowtie2index
    • Description: Validated Bowtie2 index directory confirmed to contain all necessary index files
    • Format: bowtie2index

References & Resources

  • Tool Documentation: Contact the team for details on pathChecker