Open denisalevi opened 2 weeks ago
https://github.com/snakemake/snakemake-executor-plugin-slurm/blob/cf0560cfac101af9600d7a1f7e3e21f5485d47c4/snakemake_executor_plugin_slurm/__init__.py#L74-L77
the --comment and --output flags are not escaped, which is problematic for wildcards with spaces. Modifying it to --output '{slurm_logfile}' and --comment '{job.name}' fixed the issue for me.
--comment
--output
--output '{slurm_logfile}'
--comment '{job.name}'
https://github.com/snakemake/snakemake-executor-plugin-slurm/blob/cf0560cfac101af9600d7a1f7e3e21f5485d47c4/snakemake_executor_plugin_slurm/__init__.py#L74-L77
the
--commentand--outputflags are not escaped, which is problematic for wildcards with spaces. Modifying it to--output '{slurm_logfile}'and--comment '{job.name}'fixed the issue for me.