#!/bin/bash

snakefile=$1
numprocs=$2
ref=$3
exon_bed=$4
output=$5
temp=$6
genome=$7
inputs=$8
compressed=$9

if [[ -n "$compressed" ]]; then
    comp_str="compressed=1"
fi

snakemake --snakefile "$snakefile" -j $numprocs --config inputs=$inputs $comp_str ref=$ref exon_bed=$exon_bed output=$output temp=$temp genome=$genome
