Hybrid

# The main entry point of your workflow.
# After configuring, running snakemake --cores N #give the specific number of threads

#import config
configfile: 'config.yaml'

#import rules
include: 'rules/hybridSelectLongRead2.smk'
include: 'rules/firstround.smk'
#include: 'rules/selectEndRead.smk'
include: 'rules/secondround.smk'
include: 'rules/tworoundMerge.smk'
include: 'rules/rearrangeStart.smk'
include: 'rules/hybridPolish.smk'

wildcard_constraints:
extension = '(fa|fna|fasta)',  # extension is either .fa, .fna, or .fasta

def all_input(wildcards):
    """
    Function defining all requested inputs for the rule all (below).
    """
rule all:
    input:
        "output/B-assembler.fasta"