yap demultiplex
output directory, refer to as {output_dir}
below.{output_dir}
. Each of the sub-directory is mapped together in a single job, all the steps that need to be done are written in the {output_dir}/{sub_dir}/Snakefile
, a file needed by snakemake, and contain all the commands to map the files in this sub-directory. {output_dir}/snakemake
, you should be able to find a list of snakemake commands like the above, one command for each PCR index sub-directory. You have three ways to execute these commands.