Check BWA Files Specifications
Process Details
- Name:
check_BWA_files - Process UUID:
2WpM54JN60DuDV9xdYqIfC0jCpp82L - Process Group:
Index
Overview
This process validates the availability of BWA (Burrows-Wheeler Aligner) index files required for DNA sequence alignment. The process performs a systematic check to ensure that the BWA index files exist at the specified location before proceeding with alignment operations. It includes conditional execution logic that determines whether BWA alignment should be performed based on user-specified parameters.
This process is implemented in Bash, which utilizes a custom pathChecker function to verify file system paths and index integrity.
Key Functionality
- Index File Validation: Systematically checks for the presence and accessibility of BWA index files at the specified path
- Conditional Execution Control: Evaluates the run_BWA parameter to determine if BWA alignment should proceed
- Path Verification: Uses the pathChecker function to validate folder structure and file availability for downstream BWA operations
Input/Output Specification
Inputs
Optional Inputs
- BWA Index
- Description: Pre-built BWA index files containing the reference genome in BWA-compatible format
- Format: bwaindex (folder containing .amb, .ann, .bwt, .pac, .sa files)
Outputs
- BWA Index
- Description: Validated BWA index files ready for use in alignment processes
- Format: bwaindex (folder containing BWA index components)
Parameters & Settings
This process uses internal parameter evaluation for the run_BWA setting, which controls whether BWA alignment operations should be executed. The parameter evaluation is handled automatically by the workflow logic.
References & Resources
- Tool Documentation: Contact the team for details on the pathChecker function implementation
- Related Papers: Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760. DOI: 10.1093/bioinformatics/btp324