Running the read simulation pipeline

Modifying simulation parameters

If desired, manually edit the file simulation_params.yaml

Uncomment lines as required then adjust settings as desired. Use the default values (provided) as a starting point

It is necesary to set a new “output_tag” for each run, unless “clobber” is also used, in which case it will overwrite previous runfiles of the same name, if they exist.

Running the workflow

launch the workflow with:

bash ../ALISEQ/simulate_reads.sh

Note

If you encounter the following error mesage (e.g. after a power failure or loss of network connection) Error: Directory cannot be locked..., run the following cmd before retrying

snakemake --unlock -s ../ALISEQ/scripts/simulate_reads.snk