chipseq.snakefile

configfile: "CONFIG/chipseq.yaml"
# RUNINFO
INPUTINFO = config["INPUTINFO"]
# OUTPUTPATH
alignment = config["OUTPUTPATH"]["alignment"]
macs2 = config["OUTPUTPATH"]["macs2"]
# DATAPATH
SAMPLEPATH = config["DATAPATH"]["SAMPLEPATH"]
GTF = config["DATAPATH"]["SAMPLEPATH"]
GENOME = config["DATAPATH"]["GENOME"]
INDEX = config["DATAPATH"]["INDEX"]
REFSEQ = config["DATAPATH"]["REFSEQ"]
# SAMPLEINFO
ALLSAMPLE = config["ALLSAMPLE"]
# EXNAME          = config["EXNAME"]
INPUTINFO = config["INPUTINFO"]

# PARA
THREAD = config["THREAD"]

# SOFT
BOWTIE2 = config["SOFT"]["bowtie2"]
MACS2 = config["SOFT"]["macs2"]
SAMTOOLS = config["SOFT"]["samtools"]
BAMCOVERAGE = config["SOFT"]["bamcoverage"]
COMPUTEMATRIX = config["SOFT"]["computeMatrix"]
PLOTHEATMAP = config["SOFT"]["plotHeatmap"]
PLOTPROFILE = config["SOFT"]["plotProfile"]

rule all:
    input: expand(macs2 + '/{sample}/{sample}.png', sample=INPUTINFO),
        expand(macs2 + '/{sample}/{sample}_summits.bed', sample=INPUTINFO)

include: "rules/alignment/bowtie2.rule"
include: "rules/peak/peak.rule"
include: "rules/peak/bamcoverage.rule"