pigz -> zcat | gzip

ndbrown6 · Jul 27, 2022 · 12077fb · 12077fb
1 parent eaaa6f8
commit 12077fb
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Showing 2 changed files with 9 additions and 4 deletions.
diff --git a/fastq_aligners/bwa_parallel.mk b/fastq_aligners/bwa_parallel.mk
@@ -54,10 +54,12 @@ GATK_MEM_THREAD = 2G
 
 define merge-fastq
 bwamem/$1/$1_R1.fastq.gz : $$(foreach split,$2,$$(word 1, $$(fq.$$(split))))
-	$$(call RUN,-c -n 12 -s 0.5G -m 1G -w 24:00:00 -v $(PIGZ_ENV),"$$(PIGZ) -cd -p 12 $$(^) | $$(PIGZ) -c -p 12 > $$(@)")
+	$$(call RUN,-c -n 12 -s 0.5G -m 1G -w 24:00:00 -v $(PIGZ_ENV),"set -o pipefail && \
+								       $$(PIGZ) -cd -p 12 $$(^) | $$(PIGZ) -c -p 12 > $$(@)")
 
 bwamem/$1/$1_R2.fastq.gz : $$(foreach split,$2,$$(word 2, $$(fq.$$(split))))
-	$$(call RUN,-c -n 12 -s 0.5G -m 1G -w 24:00:00 -v $(PIGZ_ENV),"$$(PIGZ) -cd -p 12 $$(^) | $$(PIGZ) -c -p 12 > $$(@)")
+	$$(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)))))

diff --git a/rna_seq/umi_tools.mk b/rna_seq/umi_tools.mk
@@ -32,14 +32,17 @@ umi_tools : $(foreach sample,$(SAMPLES),umi_tools/$(sample)/$(sample)_R1.fastq.g
 
 define merge-fastq
 umi_tools/$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 && \
+								       $$(PIGZ) -cd -p 12 $$(^) | $$(PIGZ) -c -p 12 > $$(@)")
 
 umi_tools/$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 clip-fastq
 umi_tools/$1/$1_R1_cl.fastq.gz : umi_tools/$1/$1_R1.fastq.gz umi_tools/$1/$1_R2.fastq.gz
 	$$(call RUN,-c -n 1 -s 8G -m 16G -v $(UMITOOLS_ENV),"set -o pipefail && \