snakemake_cmd.txtcontains all the snakemake command for all PCR index sub-directories.
sbatch.shis a submission script file that can automatically submit all these commands via
yap sbatchwill control the total number of jobs run in parallel on the sbatch.
output_dirfrom the remote server back to the same location. If you
rsyncto the same path, you may skip the FASTQ files because they are unchanged during mapping.