Add an optional output_dir value that specifies a directory to output results into.
To ensure that relative paths to input files/resources in config.yaml are still valid when output_dir is specified, the relevant values are resolved to absolute paths if present in the config.yaml.
If output_dir isn't specified then the output_dir/workdir is just the directory that snakemake is executed from i.e., the current working directory will be used (as is the current behaviour) and no other changes are made.
Add an optional
output_dir
value that specifies a directory to output results into.To ensure that relative paths to input files/resources in
config.yaml
are still valid whenoutput_dir
is specified, the relevant values are resolved to absolute paths if present in theconfig.yaml
.If
output_dir
isn't specified then theoutput_dir
/workdir is just the directory that snakemake is executed from i.e., the current working directory will be used (as is the current behaviour) and no other changes are made.Changes have been tested for
conda
env install.