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Flatten Cellranger Reads Specifications

Process Details

  • Name: flatten_cellranger_reads
  • Process UUID: NaVFcp0ROVMATNy5h08MU6f3nznMWq
  • Process Group: SingleCell

Overview

This process prepares Cell Ranger FASTQ files for downstream quality control analysis by renaming undetermined reads files and reorganizing the directory structure. The process prevents naming conflicts in MultiQC reports by adding unique prefixes to undetermined FASTQ files and consolidates all reads into a unified directory structure for subsequent processing steps.

This process is implemented in Bash.

Key Functionality

  • File Renaming: Renames "Undetermined" FASTQ files to prevent name collisions in MultiQC reports by adding directory-specific prefixes
  • Directory Reorganization: Creates a new "allreads" directory and moves all FASTQ files into this consolidated structure
  • Quality Control Preparation: Ensures proper file naming conventions for downstream MultiQC analysis and reporting

Input/Output Specification

Inputs

Required Inputs

  • reads
    • Description: FASTQ files from Cell Ranger output, including both sample-specific and undetermined reads
    • Format: FASTQ

Outputs

  • mate

    • Description: Mate pair information for paired-end sequencing data
    • Format: mate

  • reads

    • Description: Reorganized FASTQ files with renamed undetermined reads in a consolidated directory structure
    • Format: FASTQ

Parameters & Settings

This process runs conditionally when FastQC analysis is enabled in the pipeline configuration.

References & Resources

  • Tool Documentation: This process uses standard Bash commands for file manipulation and directory organization