Update bismark_bt2.mk

ndbrown6 · Jul 26, 2022 · 3304ccb · 3304ccb
1 parent bcb29a0
commit 3304ccb
Showing 1 changed file with 6 additions and 5 deletions.
diff --git a/fastq_aligners/bismark_bt2.mk b/fastq_aligners/bismark_bt2.mk
@@ -35,16 +35,17 @@ GATK_MEM_THREAD = 2G
 
 define merge-fastq
 bismark/$1/$1_R1.fastq.gz : $$(foreach split,$2,$$(word 1, $$(fq.$$(split))))
-	$$(call RUN,-c -n 1 -s 4G -m 6G,"set -o pipefail && \
-					 zcat $$(^) | gzip -c > $$(@)")
-
+	$$(call RUN,-c -n 12 -s 0.5G -m 1G -w 24:00:00 -v $(PIGZ_ENV),"set -o pipefail && \
+								       $$(PIGZ) -cd -p 12 $$(^) | $$(PIGZ) -c -p 12 > $$(@)")
+	
 bismark/$1/$1_R2.fastq.gz : $$(foreach split,$2,$$(word 2, $$(fq.$$(split))))
-	$$(call RUN,-c -n 1 -s 4G -m 6G,"set -o pipefail && \
-					 zcat $$(^) | 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-to-bam
 bismark/$1/$1_bismark_bt2_pe.bam : bismark/$1/$1_R1.fastq.gz bismark/$1/$1_R2.fastq.gz
 	$$(call RUN,-c -n $(BISMARK_THREADS) -s 2G -m $(BISMARK_MEM_THREAD) -v $(BISMARK_ENV),"set -o pipefail && \