diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml index 5ac42e30..3047fe96 100644 --- a/hippunfold/config/snakebids.yml +++ b/hippunfold/config/snakebids.yml @@ -291,10 +291,10 @@ parse_args: --workdir: help: | - Folder for storing working files. If not specified, a temporary folder - will be made in your system's temp directory (e.g. /tmp). You can also - use environment variables when setting the workdir, e.g. --workdir '$SLURM_TMPDIR'. - default: null + Folder for storing working files. If not specified, will be in "work/" subfolder + in the output folder. You can also use environment variables when setting the + workdir, e.g. --workdir '$SLURM_TMPDIR'. + default: work type: str diff --git a/hippunfold/workflow/Snakefile b/hippunfold/workflow/Snakefile index 5cbfc74d..6f22980a 100644 --- a/hippunfold/workflow/Snakefile +++ b/hippunfold/workflow/Snakefile @@ -95,8 +95,6 @@ wildcard_constraints: template="[a-zA-Z0-9]+", -if config["workdir"] == None: - config["workdir"] = mkdtemp() work = os.path.expandvars(config["workdir"]) root = os.path.expandvars(config["root"])