From 066aca608443097e334ad51073aa4fa624b8604d Mon Sep 17 00:00:00 2001 From: Ali Khan Date: Wed, 20 Nov 2024 22:11:11 -0500 Subject: [PATCH] remove the leading ./ from paths created in snakebids since this now results in a CRITICAL warning in snakemake --- snakebids/plugins/snakemake.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/snakebids/plugins/snakemake.py b/snakebids/plugins/snakemake.py index 30304f6c..1b7349bf 100644 --- a/snakebids/plugins/snakemake.py +++ b/snakebids/plugins/snakemake.py @@ -289,7 +289,7 @@ def finalize_config(self, config: dict[str, Any]): print(err.msg, file=sys.stderr) sys.exit(1) self.cwd = config["output_dir"] - root = Path() + root = "" #uses "" instead of Path() so we end up with filepath instead of ./filepath configfile_path = self.configfile_path or self.snakemake_dir / "snakebids.yaml" if self.configfile_outpath is None: