projects/radseq/make/cutadapter.mk

   1 RADSEQFQPATH := work/radseq
   2 WGSFQPATH := work/parents
   3
   4 ADAPTER13:=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
   5 ADAPTER15:=ACACTCTTTCCCTACACGACGCTCTTCCGATCT
   6 ADAPTER23:=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
   7 ADAPTER25:=GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
   8
   9 CUTADAPTARG:=-e 0.08 -n 2 -m 0 -O 5
  10 CUTADRADARG:=-e 0.08 -n 1 -m 0 -O 5
  11
  12 FQEXTS:=.fq.gz
  13 CUTADAPTCMD:=cutadapt
  14
  15 RADSEQFQS1 = $(foreach d,$(RADSEQFQPATH),$(wildcard $(addprefix $(d)/*,.1$(FQEXTS))))
  16 RADSEQFQS2 = $(foreach d,$(RADSEQFQPATH),$(wildcard $(addprefix $(d)/*,.2$(FQEXTS))))
  17 WGSFQS1 = $(foreach d,$(WGSFQPATH),$(wildcard $(addprefix $(d)/*,.1$(FQEXTS))))
  18 WGSFQS2 = $(foreach d,$(WGSFQPATH),$(wildcard $(addprefix $(d)/*,.2$(FQEXTS))))
  19 COMMONFQS := $(RADSEQFQS2) $(WGSFQS1) $(WGSFQS2)
  20 ALLITEMS := $(RADSEQFQS1:.1.fq.gz=.rad) $(COMMONFQS:.fq.gz=)
  21
  22 .PHONY: all clean
  23
  24 all: $(ALLITEMS)
  25 #all: $(COMMONFQS:.fq.gz=)
  26         @echo all [$@] [$<] [${MAKEOPTS}]
  27
  28 %.1: %.1.fq.gz
  29 #       @echo "1 $(CUTADAPTCMD) -a $(ADAPTER13) -g $(ADAPTER15) $(CUTADAPTARG) -o $@.cut.gz -r $@.rest.gz $< > $@.cut.log"
  30         $(CUTADAPTCMD) -a $(ADAPTER13) -g $(ADAPTER15) $(CUTADAPTARG) -o $@.cut.gz -r $@.rest.gz $< > $@.cut.log
  31         touch $@
  32
  33 %.2: %.2.fq.gz
  34 #       @echo "2 $(CUTADAPTCMD) -a $(ADAPTER23) -g $(ADAPTER25) $(CUTADAPTARG) -o $@.cut.gz -r $@.rest.gz $< > $@.cut.log"
  35         $(CUTADAPTCMD) -a $(ADAPTER23) -g $(ADAPTER25) $(CUTADAPTARG) -o $@.cut.gz -r $@.rest.gz $< > $@.cut.log
  36         touch $@
  37
  38 %.rad: %.1.fq.gz
  39 #       @echo "RAD1 $(CUTADAPTCMD) -a $(ADAPTER13) $(CUTADRADARG) -o $(@:.rad=).cut1.gz -r $(@:.rad=).rest1.gz $< > $(@:.rad=).cut1.log"
  40 #       @echo perl $(@:.rad=).cut1.gz $(@:.rad=).cutM.gz
  41 #       @echo "RAD2 $(CUTADAPTCMD) -g $(ADAPTER15) $(CUTADRADARG) -o $(@:.rad=).cut2.gz -r $(@:.rad=).rest2.gz $(@:.rad=).cutM.gz > $(@:.rad=).cut2.log"
  42         $(CUTADAPTCMD) -a $(ADAPTER13) -g $(ADAPTER15) $(CUTADAPTARG) -o $(@:.rad=.1.cut.gz) -r $(@:.rad=.1.rest.gz) $< > $(@:.rad=.1.cut.log)
  43         touch $@
  44
  45 clean:
  46         -rm $(ALLITEMS) $(COMMONFQS:.fq.gz=.rest.gz) $(COMMONFQS:.fq.gz=.cut.log)
  47         -rm $(COMMONFQS:.fq.gz=.cut.gz)