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Makefile
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Makefile
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# Test CNVkit with bigger datasets.
#
# Dependency: cnvkit.py must be in $PATH
refgenome_ucsc := ~/db/ucsc.hg19.fasta
# ------------------------------------------------------------------------------
# Cell line validation ("CL")
cl_ref_cnns := $(wildcard cell/normal/*_N.*.cnn)
cl_tcnn := cell/CL_seq.targetcoverage.cnn
cl_cnrs := build/CL_seq.cnr build/CL_acgh.cnr
cl_segs := $(cl_cnrs:.cnr=.cns)
# ------------------------------------------------------------------------------
# Targeted resequencing samples ("TR")
tr_ref_cnns := $(wildcard targeted/TR_*_N.*.cnn)
tr_tcnn := $(wildcard targeted/TR*.targetcoverage.cnn)
tr_cnrs := $(patsubst targeted/%.targetcoverage.cnn,build/%.cnr,$(tr_tcnn))
tr_segs := $(tr_cnrs:.cnr=.cns)
tr_thin_ref_cnns := $(wildcard tr-thin/TR_*_N_thin.*.cnn)
tr_thin_tcnn := $(wildcard tr-thin/TR*_thin.targetcoverage.cnn)
tr_thin_cnrs := $(patsubst tr-thin/%.targetcoverage.cnn,build/%.cnr,$(tr_thin_tcnn))
tr_thin_segs := $(tr_thin_cnrs:.cnr=.cns)
# ------------------------------------------------------------------------------
# Exome samples ("EX")
ex_ref_cnns := $(wildcard exome/EX_*_N.*.cnn)
ex_tcnn := $(wildcard exome/EX*.targetcoverage.cnn)
ex_cnrs := $(patsubst exome/%.targetcoverage.cnn,build/%.cnr,$(ex_tcnn))
ex_segs := $(ex_cnrs:.cnr=.cns)
# ------------------------------------------------------------------------------
# Action!
all: cl tr ex
.PHONY: cl
cl: heatmap-cl.pdf
.PHONY: tr
tr: heatmap-tr.pdf TR_95_T-diagram.pdf TR_95_T-scatter.pdf TR_95_T-CDK4-MDM2-scatter.pdf
.PHONY: ex
ex: $(ex_segs) heatmap-exome.pdf
.PHONY: metrics
metrics: ex-metrics.csv tr-metrics.csv cl-metrics.csv
.PHONY: clean
clean:
# Targeted
rm -vf build/TR* heatmap-tr*.pdf
# Exome
rm -vf build/EX* heatmap-exome.pdf
# Cell
rm -vf build/CL* heatmap-cl.pdf
# ------------------------------------------------------------------------------
# Standard workflow
# == Build pooled references from normal samples
reference-cell.cnn: $(cl_ref_cnns)
cnvkit.py reference $^ -f $(refgenome_ucsc) -y -o $@
reference-tr-thin.cnn: $(tr_thin_ref_cnns)
cnvkit.py reference $^ -f $(refgenome_ucsc) -y -o $@
reference-tr.cnn: $(tr_ref_cnns)
cnvkit.py reference $^ -f $(refgenome_ucsc) -y -o $@
reference-exome.cnn: $(ex_ref_cnns)
cnvkit.py reference $^ -f $(refgenome_ucsc) -y -o $@
# == Build components
intervals/reference-cl-flat.cnn:
cd intervals && $(MAKE)
build/CL_seq.cnr: build/%.cnr: cell/%.targetcoverage.cnn cell/%.antitargetcoverage.cnn reference-cell.cnn
cnvkit.py fix $^ -o $@
build/CL_acgh.cnr: cell/CL_acgh.cnr
cp $< $@
$(tr_thin_cnrs): build/%.cnr: tr-thin/%.targetcoverage.cnn tr-thin/%.antitargetcoverage.cnn reference-tr-thin.cnn
cnvkit.py fix $^ -o $@
$(tr_cnrs): build/%.cnr: targeted/%.targetcoverage.cnn targeted/%.antitargetcoverage.cnn reference-tr.cnn
cnvkit.py fix $^ -o $@
$(ex_cnrs): build/%.cnr: exome/%.targetcoverage.cnn exome/%.antitargetcoverage.cnn reference-exome.cnn
cnvkit.py fix $^ -o $@
build/CL_seq.cns $(tr_thin_segs) $(tr_segs) $(ex_segs): %.cns: %.cnr
cnvkit.py segment --drop-low $< -o $@
# Segment aCGH without filtering
build/CL_acgh.cns: build/CL_acgh.cnr
cnvkit.py segment --drop-outliers 0 $< -o $@
# == Results
heatmap-cl.pdf: $(cl_segs)
cnvkit.py heatmap -d -o $@ $^
heatmap-tr-thin.pdf: $(tr_thin_segs)
cnvkit.py heatmap -d -o $@ $(filter %_T_thin.cns,$^)
heatmap-tr.pdf: $(tr_segs)
cnvkit.py heatmap -d -o $@ $(filter %_T.cns,$^)
heatmap-tr-nod.pdf: $(tr_segs)
cnvkit.py heatmap -o $@ $(filter %_T.cns,$^)
heatmap-exome.pdf: $(ex_segs)
cnvkit.py heatmap -d -o $@ $(filter %_T.cns,$^)
cl-metrics.csv: $(cl_segs)
cnvkit.py metrics $(cl_segs:.cns=.cnr) -s $^ -o $@
tr-thin-metrics.csv: $(tr_thin_segs)
cnvkit.py metrics $(tr_thin_cnrs) -s $^ -o $@
tr-metrics.csv: $(tr_segs)
cnvkit.py metrics $(tr_cnrs) -s $^ -o $@
ex-metrics.csv: $(ex_segs)
cnvkit.py metrics $(ex_cnrs) -s $^ -o $@
# Example figures
TR_95_T-diagram.pdf: build/TR_95_T.cns build/TR_95_T.cnr
cnvkit.py diagram -s $^ -y -o $@
TR_95_T-scatter.pdf: build/TR_95_T.cns build/TR_95_T.cnr
cnvkit.py scatter -s $^ -o $@
TR_95_T-CDK4-MDM2-scatter.pdf: build/TR_95_T.cns build/TR_95_T.cnr
cnvkit.py scatter -s $^ -o $@ -c chr12:50000000-80000000 -g CDK4,MDM2