diff --git a/pixi.toml b/pixi.toml index 0b785df93..8b017bf87 100644 --- a/pixi.toml +++ b/pixi.toml @@ -37,7 +37,24 @@ test = { cmd = [ "test-data", ], clean-env = true } -fire = { cmd = "cd $INIT_CWD && snakemake -s $PIXI_PROJECT_ROOT/workflow/Snakefile" } +fire = { cmd = [ + "cd", + "$INIT_CWD", + "&&", + "snakemake", + "-s", + "$PIXI_PROJECT_ROOT/workflow/Snakefile", +] } +slurm = { cmd = [ + "cd", + "$INIT_CWD", + "&&", + "snakemake", + "-s", + "$PIXI_PROJECT_ROOT/workflow/Snakefile", + "--profile", + "$PIXI_PROJECT_ROOT/profiles/slurm-executor", +] } [dependencies] conda = "*"