Dear All
Sorry for my aive question iI'm learning ...
I have write a makefile that prepare some files:
RDIR=.
RFILES:=$(wildcard $(RDIR)/*.vcf)
OUTDIR=ORIGINAL
OUTFILES=$(patsubst %.vcf,$(OUTDIR)/%.gz,$(RFILES))
BCFTOOLS=bcftools
OUTSOMATIC=SOMATIC
OUTVARDICT=$(patsubst
$(OUTDIR)/%vardict.gz,$(OUTSOMATIC)/%.somatic.vcf,$(wildcard
$(OUTDIR)/*vardict.gz))
OUTMUTEC2=$(patsubst
$(OUTDIR)/%mutect2_all.gz,$(OUTSOMATIC)/%mutect2.somatic.vcf,$(wildcard
$(OUTDIR)/*mutect2_all.gz))
OUTVARSCAN2=$(patsubst
$(OUTDIR)/%varscan.gz,$(OUTSOMATIC)/%varscan2.somatic.vcf,$(wildcard
$(OUTDIR)/*varscan.gz))
.PHONY: all
all: $(OUTDIR) $(OUTFILES) $(OUTSOMATIC) $(OUTVARDICT) $(OUTMUTEC2)
$(OUTVARSCAN2)
$(OUTDIR)/%.gz: %.vcf
bgzip -c $< > $@
$(OUTDIR):
test -d $@ || mkdir $@
$(OUTSOMATIC):
test -d $@ || mkdir $@
$(OUTSOMATIC)/%.somatic.vcf: $(OUTDIR)/%vardict.gz
$(BCFTOOLS) view -f PASS -i 'INFO/STATUS ~ ".*Somatic"' $< > $@
$(OUTSOMATIC)/%mutect2.somatic.vcf: $(OUTDIR)/%mutect2_all.gz
$(BCFTOOLS) view -f PASS $< > $@
$(OUTSOMATIC)/%varscan2.somatic.vcf: $(OUTDIR)/%varscan.gz
$(BCFTOOLS) view -f PASS -i 'SS="2"' $< > $@
clean:
rm -rf $(OUTDIR)
rm -rf $(OUTSOMATIC)
I need to launch 3 time make -f Makefile for execute all the subroutine. How
can improve that script?
So create a drectory with the preliminary files I need for complete the other
steps. What is the right way?
thanks for any help
M
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