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Check RSEM Files Specifications

Process Details

  • Name: check_RSEM_files
  • Process UUID: QWxoBXiBzm57nDCYsDlL1sSnZ5KYb0
  • Process Group: Index

Overview

This process validates the prerequisites for RSEM (RNA-Seq by Expectation-Maximization) analysis by checking the availability and integrity of required RSEM index files. The process performs conditional validation based on the specified reference type (Bowtie, Bowtie2, or STAR) and ensures that all necessary files are present before proceeding with downstream RSEM quantification workflows.

This process is implemented in Bash, which utilizes Nextflow's pathChecker function for file validation.

Key Functionality

  • Reference Type Detection: Automatically determines the RSEM reference type (Bowtie, Bowtie2, or STAR) from configuration parameters
  • Index File Validation: Verifies the presence and accessibility of RSEM index files corresponding to the selected reference type
  • Path Resolution: Uses pathChecker function to generate appropriate commands for RSEM analysis execution
  • Conditional Execution: Only runs when RSEM analysis is enabled in the pipeline configuration

Input/Output Specification

Inputs

Optional Inputs

  • RSEM Index
    • Description: Pre-built RSEM index files for transcript quantification
    • Format: rsemIndex (directory containing index files)

Outputs

  • RSEM Index
    • Description: Validated RSEM index files ready for quantification analysis
    • Format: rsemIndex (directory containing index files)

References & Resources

  • Tool Documentation: Contact the team for details on RSEM index validation procedures
  • Related Papers: Li, B., & Dewey, C. N. (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics, 12(1), 323.