snakemake-paired-sample

paired-sample2.py

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}")

paired-samples.py

# 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}
	    """