OUTPUT_DIR=/home/marykt/gotcloudTutorial
UMAKE_ROOT=/usr/local/gotcloud

.DELETE_ON_ERROR:

all: all20

all20: thunder20

thunder20: $(OUTPUT_DIR)/thunder/chr20/GBR/thunder/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz.tbi

$(OUTPUT_DIR)/thunder/chr20/GBR/thunder/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz.tbi: $(OUTPUT_DIR)/thunder/chr20/GBR/thunder/chr20.filtered.PASS.beagled.GBR.thunder.1.vcf.gz.OK
	perl $(UMAKE_ROOT)/scripts/ligateVcf.pl $(OUTPUT_DIR)/thunder/chr20/GBR/thunder/chr20.filtered.PASS.beagled.GBR.thunder.1.vcf.gz 2> $(OUTPUT_DIR)/thunder/chr20/GBR/thunder/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz.err | $(UMAKE_ROOT)/bin/bgzip -c > $(OUTPUT_DIR)/thunder/chr20/GBR/thunder/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz
	$(UMAKE_ROOT)/bin/tabix -f -pvcf $(OUTPUT_DIR)/thunder/chr20/GBR/thunder/chr20.filtered.PASS.beagled.GBR.thunder.vcf.gz

$(OUTPUT_DIR)/thunder/chr20/GBR/thunder/chr20.filtered.PASS.beagled.GBR.thunder.1.vcf.gz.OK:
	mkdir --p $(OUTPUT_DIR)/thunder/chr20/GBR/thunder
	$(UMAKE_ROOT)/bin/thunderVCF -r 10 --phase --dosage --inputPhased --shotgun /home/marykt/gotcloudTutorial/thunder/chr20/GBR/split/chr20.filtered.PASS.beagled.GBR.split.1.vcf.gz -o $(OUTPUT_DIR)/thunder/chr20/GBR/thunder/chr20.filtered.PASS.beagled.GBR.thunder.1 > $(OUTPUT_DIR)/thunder/chr20/GBR/thunder/chr20.filtered.PASS.beagled.GBR.thunder.1.out 2> $(OUTPUT_DIR)/thunder/chr20/GBR/thunder/chr20.filtered.PASS.beagled.GBR.thunder.1.err
	touch $(OUTPUT_DIR)/thunder/chr20/GBR/thunder/chr20.filtered.PASS.beagled.GBR.thunder.1.vcf.gz.OK