How to deal with paired samples for snakemake

I am currently experimenting snakemake for pipelines. We will have paired samples when processing data. e.g. ChIP-seq (IP vs Input), DNA-seq (Normal vs Tumor). How to specify them in snakemake?
The trick is to use a python dictionary to pair samples and a function to define Input files.

I will show an toy example with ChIP-seq processing.

	aDict = {"B":"inputG1", "A":"inputG1", "C":"inputG2"}
	rule all:
	input: ["C.bed", "A.bed", "B.bed"]
	def get_files(wildcards):
	case = wildcards.case
	control = aDict[case]
	return [case + ".sorted.bam", control + ".sorted.bam"]
	rule call_peak:
	input: get_files
	output: "{case}.bed"
	run:
	case = input[0]
	control = input[1]
	shell("echo macs14 -t {case} -c {control} -n {wildcards.case}")
	shell("touch {output}")

view raw paired-sample2.py hosted with ❤ by GitHub

	# read https://groups.google.com/forum/#!searchin/snakemake/dependencies/snakemake/iDnr3PIcsfE/x-qQvzWBBgAJ
	# https://groups.google.com/forum/#!searchin/snakemake/dependencies/snakemake/1QelazgzilY/oBgZoP19BL4J
	aDict = {"B":"inputG1", "A":"inputG1", "C":"inputG2"}
	rule all:
	input: ["C.bed", "A.bed", "B.bed"]
	def get_files(wildcards):
	case = wildcards.case
	control = aDict[case]
	return [case + ".sorted.bam", control + ".sorted.bam"]
	rule call_peak:
	input: get_files
	output: "{case}.bed"
	shell:
	"""
	echo macs14 -t {input[0]} -c {input[1]} -n {wildcards.case}
	touch {output}
	"""

view raw paired-samples.py hosted with ❤ by GitHub