Job configurations for the scRNAbox pipeline

• Introduction
• General configurations
• Step configurations

---

Introduction

Upon running Step 0, the scrnabox_config.ini file is automatically deposited into ~/working_directory/job_info/configs:

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
SCRNA_METHOD=SCRNA
############# 

############# [step2]
# THREADS_ARRAY["step_2"]=10
# MEM_ARRAY["step_2"]=16g
# WALLTIME_ARRAY["step_2"]=00-05:00 

############# [step3]
# THREADS_ARRAY["step_3"]=10
# MEM_ARRAY["step_3"]=16g
# WALLTIME_ARRAY["step_3"]=00-05:00 

############# [step4]
# THREADS_ARRAY["step_4"]=10
# MEM_ARRAY["step_4"]=45g
# WALLTIME_ARRAY["step_4"]=00-05:00 

############# [step5]
# THREADS_ARRAY["step_5"]=10
# MEM_ARRAY["step_5"]=16g
# WALLTIME_ARRAY["step_5"]=00-05:00 

#############[step6]
# THREADS_ARRAY["step_6"]=10
# MEM_ARRAY["step_6"]=16g
# WALLTIME_ARRAY["step_6"]=00-05:00 

############# [step7]
# THREADS_ARRAY["step_7_markergsea"]=4
# MEM_ARRAY["step_7_markergsea"]=16g
# WALLTIME_ARRAY["step_7_markergsea"]=00-05:00

# THREADS_ARRAY["step_7_knownmarkers"]=4
# MEM_ARRAY["step_7_knownmarkers"]=16g
# WALLTIME_ARRAY["step_7_knownmarkers"]=00-05:00

# THREADS_ARRAY["step_7_referenceannotation"]=10
# MEM_ARRAY["step_7_referenceannotation"]=150g
# WALLTIME_ARRAY["step_7_referenceannotation"]=00-12:00

# THREADS_ARRAY["step_7_annotate"]=4
# MEM_ARRAY["step_7_annotate"]=16g
# WALLTIME_ARRAY["step_7_annotate"]=00-05:00

############# [step8]
# THREADS_ARRAY["step_8_addmeta"]=4
# MEM_ARRAY["step_8_addmeta"]=16g
# WALLTIME_ARRAY["step_8_addmeta"]=00-12:00 

# THREADS_ARRAY["step_8_rundge"]=4
# MEM_ARRAY["step_8_rundge"]=40g
# WALLTIME_ARRAY["step_8_rundge"]=00-12:00 

############# [integrate]
# THREADS_ARRAY["integrate"]=10
# MEM_ARRAY["integrate"]=40g
# WALLTIME_ARRAY["integrate"]=00-04:00 

The scrnabox_config.ini defines the parameters for each Job submission to the Slurm Workload Manager. Prior to performing their analysis with the scRNAbox pipeline, users should modify this file to adjust the General configurations and Analytical Step configurations.

---

General configurations

The following parameters must be adjusted by the user:

1) ACCOUNT: the name of the account holder for the HPC system;
2) MODULEUSE: the path to the environmental module;
3) CELLRANGER: the path to CellRanger from the environmental module directory;
4) CELLRANGER_VERSION: the version of CellRanger;
5) R_VERSION: the version of R installed on the HPC system (must be v4.2 or greater);
6) R_LIB_PATH: the path to the R library containing the required R packages for running scRNAbox;
7) SCRNA_METHOD: The analysis track to use (SCRNA or HTO). This will be automatically defined upon running Step 0.

---

Step configurations

Each step of the scRNAbox pipeline has three configuartion parameters:

1) THREADS_ARRAY: number of CPUs for the job;
2) MEM_ARRAY: amount of memory (RAM) for the job;
3) WALLTIME_ARRAY: amount of time for the job.

In the original scrnabox_config.ini file, the configuration parameters for each step will be commented out and the default configurations will be used. If users need to change the configurations for any step, they can uncomment the line of code and define the parameter:

# orginal scrnabox_config.ini
#THREADS_ARRAY["step_2"]=4
#MEM_ARRAY["step_2"]=16g
#WALLTIME_ARRAY["step_2"]=00-05:00 

# modified scrnabox_config.ini
THREADS_ARRAY["step_2"]=8
MEM_ARRAY["step_2"]=24g
WALLTIME_ARRAY["step_2"]=00-10:00