Job configurations for the scRNAbox pipeline


Introduction

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

ACCOUNT=HPC_account_owner_name
MODULEUSE=/cvmfs/soft.mugqic/CentOS6/modulefiles
MODULECELLRANGER=mugqic/cellranger/5.0.1
R_VERSION=4.2.1
R_LIB_PATH=/path/to/R/library
SCRNA_METHOD=SCRNA
############# 

############# [step2]
#THREADS_ARRAY["step_2"]=4
#MEM_ARRAY["step_2"]=16g
#WALLTIME_ARRAY["step_2"]=00-05:00 

############# [step3]
#THREADS_ARRAY["step_3"]=4
#MEM_ARRAY["step_3"]=16g
#WALLTIME_ARRAY["step_3"]=00-05:00 

############# [step4]
#THREADS_ARRAY["step_4"]=4
#MEM_ARRAY["step_4"]=45g
#WALLTIME_ARRAY["step_4"]=00-05:00 

############# [step5]
#THREADS_ARRAY["step_5"]=4
#MEM_ARRAY["step_5"]=45g
#WALLTIME_ARRAY["step_5"]=00-05:00 

#############[step6]
#THREADS_ARRAY["step_6"]=4
#MEM_ARRAY["step_6"]=16g
#WALLTIME_ARRAY["step_6"]=00-05:00 

############# [step7]
#THREADS_ARRAY["step_7marker"]=4
#MEM_ARRAY["step_7marker"]=40g
#WALLTIME_ARRAY["step_7marker"]=00-1:00 

#THREADS_ARRAY["step_7enrich"]=10
#MEM_ARRAY["step_7enrich"]=15g
#WALLTIME_ARRAY["step_7enrich"]=00-01:00 

#THREADS_ARRAY["step_7fta"]=4
#MEM_ARRAY["step_7fta"]=150g
#WALLTIME_ARRAY["step_7fta"]=00-09:00 

############# [step8]
#THREADS_ARRAY["step_8_dgelist"]=4
#MEM_ARRAY["step_8_dgelist"]=40g
#WALLTIME_ARRAY["step_8_dgelist"]=00-12:00 

############# [step8]
#THREADS_ARRAY["step_8_cont"]=10
#MEM_ARRAY["step_8_cont"]=40g
#WALLTIME_ARRAY["step_8_cont"]=00-12:00 

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 the this file to adjust the General configurations and Analytical Step configurations.


General configurations

The following general configuration parameters must be adjusted by the user:

1) ACCOUNT: the name of the account for the HPC system;
2) MODULEUSE:
3) MODULECELLRANGER:
4) R_VERSION: the version of R installed on the HPC system;
5) R_LIB_PATH: the path to the R library containing the required R packages for running scRNAbox;
6) SCRNA_METHOD: The Analytical Track used for analysis. This will be automatically defined upon running Step 0.


Analytical Step configurations

Each Analytical 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 Analytical Step will be commented out and the default configurations will be used. If users need to change the configurations for any Analytical Step, they may 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