Included Scripts

Script	Description	Usage
ashe_report_pdf.sh	Iterates of Ashe Pipeline output and creates PDF reports for each sample using an Rmd script	Usage: bash ashe_report_pdf.sh "outdir"
entrez_pull.sh	Obtains the taxonomy for NCBI accession numbers that is used for creating new MOB Suite plasmid databases	Usage: bash entrez_pull.sh "input_file" "ouput_file"
run_ashe.sh	Bash script used to run the Ashe Pipeline, an updated version of the ashe_report_pdf.sh, with an addition of the Nextflow command to run the pipeline and a sleep function to wait for the pipeline to finish	Usage: bash run_ashe.sh "input_sheet" "output_dir" "cpus" "memory" "optional -resume"