Snakefile example

snakefile

CHUNKSIZE=250
NCHUNK=864
CHUNK=range(0,NCHUNK)


rule all:
	input:
		"instrument_specificity_analysis.html"

rule dl:
	output:
		"../data/ld/AFR.bed"
	shell:
		"mkdir -p ../data/ld; cd ../data/ld; wget http://fileserve.mrcieu.ac.uk/ld/1kg.v3.tgz; tar xzvf 1kg.v3.tgz"

rule ld:
	input:
		"../data/ld/AFR.bed"
	output:
		"../data/ld/maps.rdata"
	shell:
		"Rscript generate_ld.r"

rule instrument_specificity:
	input:
		"../data/ld/maps.rdata",
		"instrument_specificity.r"
	output:
		"../results/instrument_specificity/{CHUNK}.rdata"
	shell:
		"Rscript instrument_specificity.r {wildcards.CHUNK} {CHUNKSIZE}"

rule aggregate:
	input:
		expand("../results/instrument_specificity/{CHUNK}.rdata", CHUNK=CHUNK)
	output:
		"../results/instrument_specificity.rdata"
	shell:
		"Rscript instrument_specificity_aggregate.r {NCHUNK}"

rule analysis:
	input:
		"../results/instrument_specificity.rdata",
		"instrument_specificity_analysis.rmd"
	output:
		"instrument_specificity_analysis.html"
	shell:
		"Rscript -e 'rmarkdown::render(\"instrument_specificity_analysis.rmd\")'"