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Makefile.mak
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# Variables
NTASKS = 1
TIME = 24:00:00
MEM = 16G # specify memory
PARTITION = standard # set this to the partition you are using
NUM_SAMPLES = 10 # set this to the number of samples you are running
# Targets
.PHONY: all help 1-part1 remove_recurrent 1-part2 2-compare 3-stratification filter merge
all: 1-part1 remove_recurrent 1-part2 2-compare 3-stratification filter merge
help:
@echo "Makefile targets:"
@echo " all - Run all parts of the workflow in sequence."
@echo " 1-part1 - Run the 1-Optical-Mapping-SV-part1.sh script."
@echo " remove_recurrent - Run the Bionano-remove-recurrent.sh script."
@echo " 1-part2 - Run the 1-Optical-Mapping-SV-part2.sh script."
@echo " 2-compare - Run the 2-compare.sh script."
@echo " 3-stratification - Run the 3-stratification.sh script."
@echo " filter - Run the filter-sv.sh script."
@echo " merge - Run the merge-sv.sh script."
1-part1:
sbatch --ntasks=$(NTASKS) -t $(TIME) --mem=$(MEM) --partition=$(PARTITION) --job-name=1-Optical-Mapping-part1 \
-o /scripts/Bionano/script.pack/out_err_files/%J.%N.out -e /scripts/Bionano/script.pack/out_err_files/%J.%N.err \
--array=1-$(NUM_SAMPLES) 1-Optical-Mapping-SV-part1.sh
remove_recurrent: 1-part1
sbatch --ntasks=$(NTASKS) -t $(TIME) --mem=$(MEM) --partition=$(PARTITION) --job-name=remove-recurrent \
-o /scripts/Bionano/script.pack/out_err_files/%J.%N.out -e /scripts/Bionano/script.pack/out_err_files/%J.%N.err \
Bionano-remove-recurrent.sh
1-part2: remove_recurrent
sbatch --ntasks=$(NTASKS) -t $(TIME) --mem=$(MEM) --partition=$(PARTITION) --job-name=1-Optical-Mapping-part2 \
-o /scripts/Bionano/script.pack/out_err_files/%J.%N.out -e /scripts/Bionano/script.pack/out_err_files/%J.%N.err \
1-Optical-Mapping-SV-part2.sh
2-compare: 1-part2
sbatch --ntasks=$(NTASKS) -t $(TIME) --mem=$(MEM) --partition=$(PARTITION) --job-name=2-compare \
-o /scripts/Bionano/script.pack/out_err_files/%J.%N.out -e /scripts/Bionano/script.pack/out_err_files/%J.%N.err \
--array=1-$(NUM_SAMPLES) 2-compare.sh
3-stratification: 2-compare
sbatch --ntasks=$(NTASKS) -t $(TIME) --mem=$(MEM) --partition=$(PARTITION) --job-name=3-stratifications \
-o /scripts/Bionano/script.pack/out_err_files/%J.%N.out -e /scripts/Bionano/script.pack/out_err_files/%J.%N.err \
--array=1-$(NUM_SAMPLES) 3-stratifications.sh
filter: 3-stratification
sbatch --ntasks=$(NTASKS) -t $(TIME) --mem=$(MEM) --partition=$(PARTITION) --job-name=filter-sv \
-o /scripts/Bionano/script.pack/out_err_files/%J.%N.out -e /scripts/Bionano/script.pack/out_err_files/%J.%N.err \
scripts/WGS/SV/filter-sv.sh
merge: filter
sbatch --ntasks=$(NTASKS) -t $(TIME) --mem=$(MEM) --partition=$(PARTITION) --job-name=merge-sv \
-o /scripts/Bionano/script.pack/out_err_files/%J.%N.out -e /scripts/Bionano/script.pack/out_err_files/%J.%N.err \
scripts/WGS/SV/merge-sv.sh