Step 0: scRNAbox pipeline set up

Step 0 initiates the pipeline and sets up the working directory by depositing the required files. In Step 0, users must determine whether they want to use the scRNAbox container (--container TRUE), whether to use the SLURM workload manager (--jobmode Slurm) or a stand alone system (--jobmode local), and whether to use the standard analysis track (--method SCRNA) or HTO analysis track (--method HTO).

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Running Step 0

Create a dedicated folder for the analysis (hereafter referred to as the working directory). Then, export the path to the working directory and the path to scrnabox.slurm:

mkdir working_directory
cd /pathway/to/working_directory

export SCRNABOX_HOME=/pathway/to/scrnabox.slurm
export SCRNABOX_PWD=/pathway/to/working_directory

Next, run Step 0. In this example, we are electing to use the scRNAbox container (--container TRUE), the Slurm workload manager (--jobmode Slurm), and the standard analysis track (--method SCRNA):

cd /pathway/to/working_directory 

bash $SCRNABOX_HOME/launch_scrnabox.sh -d ${SCRNABOX_PWD} --steps 0 --container TRUE --jobmode Slurm --method SCRNA 

After running Step 0, the structure of the working directory should be:

 working_directory
 └── job_info
     ├── configs
     ├── logs
     └── parameters

• The configs/ directory contains the scrnabox_config.ini file which allows users to specify their job allocations (memory, threads, and walltime) for each analytical step using the Slurm Workload Manager;
  
• The logs/ directory records the events of each analytical step;
  
• The parameters/ directory contains adjustable, step-specific text files which allow users to define the execution parameters for each analytical step.
  

Next, navigate to the scrnabox_config.ini file in ~/working_directory/job_info/configs to define the HPC account holder (ACCOUNT), the path to the environmental module (MODULEUSE), the path to CellRanger from the environmental module directory (CELLRANGER), CellRanger version (CELLRANGER_VERSION), R version (R_VERSION), and the path to the R library (R_LIB_PATH):

ACCOUNT=account-name
MODULEUSE=/path/to/environmental/module (e.g. /cvmfs/soft.mugqic/CentOS6/modulefiles)
CELLRANGER=/path/to/cellranger/from/module/directory (e.g. mugqic/cellranger)
CELLRANGER_VERSION=5.0.1
R_VERSION=4.2.1
R_LIB_PATH=/path/to/R/library

Note: The text files can be opened and modified through nano, vim, or a file manager system like cyberduck.
Note: For more information regarding the configuration file, please see the Job cofigurations sections of the scRNAbox documentation.