Some steps, like assembly, may have an optional temporary directory. If
specified in the configuration or as an environmental variable
TMPDIR``|``TEMP``|``TMP], the step will use this directory rather than
the current working directory.
Default: the working directory
Shell Command Prefix¶
This allows the user to prepend something to each command. In our case, we reserve a SLURM allocation, then submit jobs across the reservation with:
prefix: srun --exclusive -N1 -n1 -c__threads__
threads from the top-level of the configurations is prepended to each
multi-threaded step as the workflow is executed.
Additionally, for multi-threaded jobs, the user can set environmental variable SHPFXM while for single-threaded jobs the user can set SHPFXS as the command prefix.