A6a_nextpolish_run.cfg

job_type = local
job_prefix = nextPolish_Hsub
task = best
rewrite = yes
rerun = 3
parallel_jobs = 6
multithread_jobs = 5
genome = /home/projects/ku_00039/people/joeviz/GAGA_genomes/Genome_assemblies/PacBio_nonpolished_assemblies/GAGA-0098_Harpagoxenus_sublaevis_unpolished.fasta #genome file
genome_size = auto
workdir = nextpolish_hsub
polish_options = -p {multithread_jobs}
sgs_fofn = ./sgs.fofn
sgs_options = -max_depth 100 -bwa