import rnftools

rnftools.mishmash.sample("SE_reads",reads_in_tuple=1)

# put your reference genome here
fa="../reference.fa"

rnftools.mishmash.DwgSim(
	fasta=fa,
	number_of_read_tuples=1000,
	read_length_1=100,
	read_length_2=0,
	mutation_rate=0.09,
)

include: rnftools.include()
rule: input: rnftools.input()
