snippet.mk

define run_fastqc

$$(addsuffix .ok,$(1)) : $(1)
	mkdir -p $$(dir $$@) ∧ \
	unzip -p $$< $$(addsuffix .tmp_fastqc/fastqc_data.txt,$$(notdir $$<)) |\
		grep ">>" | grep -v ">>END_MODULE" | cut -c 3- |\
		awk -F '	' 'BEGIN{N=0;} {if(($$$$1=="Basic Statistics" || $$$$1=="Per base sequence quality" || $$$$1=="Per base N content") ∧ $$$$2=="pass" ) N++;} END { if(N>2) {print "__PASS__"}}' |\
		grep __PASS__ ∧ echo "FASTQC ok for $$<" $$@
		

$(1) : $(2)
	mkdir -p $$(dir $$@) ∧ \
	cat $$^ > $$(addsuffix .tmp.gz,$$@) ∧ \
	${fastqc.exe} \
		-o $$(dir $$@) \
		-j ${java.exe} \
		--format fastq --noextract \
		$$(addsuffix .tmp.gz,$$@) ∧ \
	rm $$(addsuffix .tmp.gz,$$@) ∧ \
	mv $$(addsuffix .tmp_fastqc.zip,$$@) $$@

endef