Update fgbio_access.mk

ndbrown6 · Jul 26, 2022 · 003e7c8 · 003e7c8
1 parent 3304ccb
commit 003e7c8
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/msk_access/fgbio_access.mk b/msk_access/fgbio_access.mk
@@ -81,14 +81,17 @@ TARGETS_LIST ?= $(HOME)/share/lib/resource_files/MSK-ACCESS-v1_0-probe-A.sorted.
 
 define merge-fastq
 fgbio/$1/$1_R1.fastq.gz : $$(foreach split,$2,$$(word 1, $$(fq.$$(split))))
-	$$(call RUN,-c -n 1 -s 4G -m 6G -w 72:00:00,"zcat $$(^) | gzip -c > $$(@)")
+	$$(call RUN,-c -n 12 -s 0.5G -m 1G -w 24:00:00 -v $(PIGZ_ENV),"set -o pipefail && \
+								       $$(PIGZ) -cd -p 12 $$(^) | $$(PIGZ) -c -p 12 > $$(@)")
 
 fgbio/$1/$1_R2.fastq.gz : $$(foreach split,$2,$$(word 2, $$(fq.$$(split))))
-	$$(call RUN,-c -n 1 -s 4G -m 6G -w 72:00:00,"zcat $$(^) | gzip -c > $$(@)")
+	$$(call RUN,-c -n 12 -s 0.5G -m 1G -w 24:00:00 -v $(PIGZ_ENV),"set -o pipefail && \
+								       $$(PIGZ) -cd -p 12 $$(^) | $$(PIGZ) -c -p 12 > $$(@)")
 endef
 $(foreach sample,$(SAMPLES),\
 		$(eval $(call merge-fastq,$(sample),$(split.$(sample)))))
 
+
 define fastq-2-bam
 fgbio/$1/$1_fq.bam : fgbio/$1/$1_R1.fastq.gz fgbio/$1/$1_R2.fastq.gz
 	$$(call RUN,-c -n 1 -s 8G -m 16G,"set -o pipefail && \