### 
#default: all
SHELL = /bin/bash
ifdef SLURMMASTER
	SHELL=srun
	.SHELLFLAGS= -N1 --cpus-per-task=1 bash -c 
endif
$(info $(SHELL))
USR = $(shell whoami)
INCLMK = 
include $(INCLMK)
### may override on cl
GZTAB=1
PREFIX = 
SUFFIX = 
PROJ = mktest
INDIR = .
OUTDIR = .
LOGDIR = $(OUTDIR)
TMPDIR = /tmp/$(USR)/$(PROJ)
###
inFile = $(wildcard $(INDIR)/$(PREFIX)*$(SUFFIX))
#$(info $(inBam))
o0 = $(addprefix $(OUTDIR)/, $(patsubst %$(SUFFIX),%-norm$(SUFFIX),$(notdir $(inFile))))
#$(info $(o0))
.DELETE_ON_ERROR:

all: $(o0)

ifeq ($(GZTAB),1)
$(OUTDIR)/%-norm$(SUFFIX): $(INDIR)/%$(SUFFIX)
	mkdir -p $(LOGDIR)
	mkdir -p $(TMPDIR)
	mkdir -p $(OUTDIR)
	$(VT) normalize -r $(GENOMEREF) -q -o - $< | bgzip > $@ 
	$(TABIX) -p vcf $@
else
$(OUTDIR)/%-norm$(SUFFIX): $(INDIR)/%$(SUFFIX)
	mkdir -p $(LOGDIR)
	mkdir -p $(TMPDIR)
	mkdir -p $(OUTDIR)
	$(VT) normalize -r $(GENOMEREF) -q -o $@ $<
endif

### 
#default: all
SHELL = /bin/bash
ifdef SLURMMASTER
	SHELL=srun
	.SHELLFLAGS= -N1 --cpus-per-task=1 bash -c 
endif
$(info $(SHELL))
USR = $(shell whoami)
INCLMK = 
include $(INCLMK)
### may override on cl
GZTAB=1
PREFIX = 
SUFFIX = 
PROJ = mktest
INDIR = .
OUTDIR = .
LOGDIR = $(OUTDIR)
TMPDIR = /tmp/$(USR)/$(PROJ)
###
inFile = $(wildcard $(INDIR)/$(PREFIX)*$(SUFFIX))
#$(info $(inBam))
o0 = $(addprefix $(OUTDIR)/, $(patsubst %$(SUFFIX),%-norm$(SUFFIX),$(notdir $(inFile))))
#$(info $(o0))
.DELETE_ON_ERROR:

all: $(o0)

ifeq ($(GZTAB),1)
$(OUTDIR)/%-norm$(SUFFIX): $(INDIR)/%$(SUFFIX)
	mkdir -p $(LOGDIR)
	mkdir -p $(TMPDIR)
	mkdir -p $(OUTDIR)
	vt normalize -r $(GENOMEREF) -q -o - $< | bgzip > $@ 
	tabix -p vcf $@
else
$(OUTDIR)/%-norm$(SUFFIX): $(INDIR)/%$(SUFFIX)
	mkdir -p $(LOGDIR)
	mkdir -p $(TMPDIR)
	mkdir -p $(OUTDIR)
	vt normalize -r $(GENOMEREF) -q -o $@ $<
endif

Revert "Added references to vt,tabix and bgzip so that only paths in include.mk need to be updated"
Revert "Added references to vt,tabix and bgzip so that only paths in include.mk need to be updated"

This reverts commit e0b44acbab24407e664d09d84c62335d2eefca03.
