makefiles/cutadapter.mk

   1 RADSEQFQPATH := fqrad
   2 WGSFQPATH := fqwgs
   3
   4 ADAPTER13:=AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATC
   5 ADAPTER15:=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
   6 ADAPTER23:=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
   7 ADAPTER25:=GATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
   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: $(ALLITEMS)
  25         @echo all [$@] [$<] [${MAKEOPTS}]
  26
  27 %.1: %.1.fq.gz
  28         $(CUTADAPTCMD) -a $(ADAPTER13) -g $(ADAPTER15) $(CUTADAPTARG) -o $@.cut.gz -r $@.rest.gz --info-file=$@.nfo.gz $< > $@.cut.log
  29         touch $@
  30
  31 %.2: %.2.fq.gz
  32         $(CUTADAPTCMD) -a $(ADAPTER23) -g $(ADAPTER25) $(CUTADAPTARG) -o $@.cut.gz -r $@.rest.gz --info-file=$@.nfo.gz $< > $@.cut.log
  33         touch $@
  34
  35 %.rad: %.1.fq.gz
  36         $(CUTADAPTCMD) -a $(ADAPTER13) -g $(ADAPTER15) $(CUTADAPTARG) -o $(@:.rad=.1.cut.gz) -r $(@:.rad=.1.rest.gz) --info-file=$(@:.rad=.1.nfo.gz) $< > $(@:.rad=.1.cut.log)
  37         touch $@
  38
  39 clean:
  40         -rm $(ALLITEMS) $(COMMONFQS:.fq.gz=.rest.gz) $(COMMONFQS:.fq.gz=.cut.log)
  41         -rm $(COMMONFQS:.fq.gz=.cut.gz)