Segpy configuration parameters

The configs directory produced after initiating the Segpy pipeline (step 0) contains the segpy.config.ini, which contains execution parameters that users must modify prior to running their analysis.

The segpy.config.ini can be modified using the following command:

# 1) Open .ini file to edit with nano
nano $PWD/configs/segpy.config.ini

# 2) Make appropriate changes.

# 3) Save and exit the .ini file with ctrl+0, enter ,ctrl+x

The following parameters are adjustable for the Segpy pipeline:

Parameter	Default	Explanation
CONTAINER_MODULE	CONTAINER_MODULE='apptainer/1.2.4'	The version of Singularity/Apptainer loaded onto your system.
ACCOUNT	ACCOUNT=user	Your SLURM user account.
CSQ_VEP	CSQ=TRUE	Whether or not to include variant annotations from VEP in the output file.
GRCH	GRCH=GRCh38	Reference genome version (GRCh38 or GRCh37).
AFFECTEDS_ONLY	AFFECTEDS_ONLY=FALSE	Whether or not to only include families with at least one affected individual.
FILTER_VARIANT	FILTER_VARIANT=TRUE	Filter the output file using relevant variant count values. See Step 3: Parse output file for more information.
RETRIEVE_SAMPLE_ID	RETRIEVE_SAMPLE_ID=TRUE	Whether or not to retain SampleIDs in the final output file.
JAVATOOLOPTIONS	JAVATOOLOPTIONS="-Xmx6g"	Java Virtual Machine (JVM) configuration setting. For most use cases the default value will be appropriate.
WALLTIME_ARRAY["step1"]	WALLTIME_ARRAY["step1"]=00-5:00	Number of CPUs for the step 1 job sumission.
THREADS_ARRAY["step1"]	THREADS_ARRAY["step1"]=8	Amount of memory (RAM) for the step 1 job sumission.
MEM_ARRAY["step1"]	MEM_ARRAY["step1"]=10g	Amount of time for the step 1 job sumission.
WALLTIME_ARRAY["step2"]	WALLTIME_ARRAY["step2"]=00-5:00	Number of CPUs for the step 2 job sumission.
THREADS_ARRAY["step2"]	THREADS_ARRAY["step2"]=8	Amount of memory (RAM) for the step 2 job sumission.
MEM_ARRAY["step2"]	MEM_ARRAY["step2"]=10g	Amount of time for the step 2 job sumission.
WALLTIME_ARRAY["step3"]	WALLTIME_ARRAY["step3"]=00-5:00	Number of CPUs for the step 3 job sumission.
THREADS_ARRAY["step3"]	THREADS_ARRAY["step3"]=8	Amount of memory (RAM) for the step 3 job sumission.
MEM_ARRAY["step3"]	MEM_ARRAY["step3"]=10g	Amount of time for the step 3 job sumission.