This repository contains a Nextflow workflow to run different simulated experiments with BOSS-RUNS. It combines the creation of simulated reads based on benchmark vcf calls using Nanosim, the preprocessing needed to run a BOSS-RUNS simulated run (reimplementation of prepare_simulation_data.smk) the sequencing and then the analysis of the run (reimplementation of the BOSS_Simulation_Example repository.
This pipeline requires the BOSS-RUNS and NanoSim repositories to be installed. It also requires a number of other programmes ideally in separate environments as managed by conda, documentation on this to follow.