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