Advanced Options

Temporary Directory

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

temporary_directory: /scratch

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__

And 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.

Default: None