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Check Sequential Mapping Indexes Specifications

Process Details

  • Name: Check Sequential Mapping Indexes
  • Process UUID: 17fc801c-e169-11e9-be30-e0aab38271b1
  • Process Group: Index

Overview

This process validates the availability and integrity of all index files required for sequential mapping workflows. It systematically checks for the presence of common database files, Bowtie indexes, Bowtie2 indexes, and STAR indexes, ensuring that all necessary components are properly configured before initiating sequential mapping analyses.

This process is implemented in Bash, which performs path validation and index verification operations.

Key Functionality

  • Index Validation: Verifies the existence and accessibility of all sequential mapping index files
  • Path Checking: Validates file paths for common databases, Bowtie, Bowtie2, and STAR indexes
  • Conditional Execution: Only runs when sequential mapping is enabled in the pipeline configuration
  • Error Prevention: Prevents downstream failures by ensuring all required indexes are available before analysis begins

Input/Output Specification

Inputs

Optional Inputs

  • Common Database

    • Description: Directory containing common reference databases used across mapping tools
    • Format: Directory

  • Bowtie Index

    • Description: Bowtie aligner index files for short read mapping
    • Format: Bowtie Index

  • Bowtie2 Index

    • Description: Bowtie2 aligner index files for gapped alignment
    • Format: Bowtie2 Index

  • STAR Index

    • Description: STAR aligner index files for splice-aware RNA-seq alignment
    • Format: STAR Index

Outputs

  • Common Database

    • Description: Validated common reference database directory
    • Format: Directory

  • Bowtie Index

    • Description: Verified Bowtie aligner index files
    • Format: Bowtie Index

  • Bowtie2 Index

    • Description: Verified Bowtie2 aligner index files
    • Format: Bowtie2 Index

  • STAR Index

    • Description: Verified STAR aligner index files
    • Format: STAR Index

References & Resources

  • Tool Documentation: Contact the team for details on pathChecker