remove l flag and add slurmqos

Author: mathiasbio

BALSAMIC/models/sbatchsubmitter.py

@@ -65,7 +65,7 @@ def _build_sbatch_header(self) -> str:
           - optional partition if `self.headjob_partition` is set
         """
         lines = [
-            "#!/bin/bash -l",
+            "#!/bin/bash",
             f"#SBATCH --account={self.account}",
             f"#SBATCH --job-name=BALSAMIC_snakemake_submit.{self.case_id}.%j",
             f"#SBATCH --output={self.log_path}/BALSAMIC_snakemake_submit.{self.case_id}.%j.out",

BALSAMIC/models/snakemake.py

@@ -137,7 +137,7 @@ def get_command(self) -> str:
 
     def get_slurm_job_arguments(self) -> str:
         return (
-            f'--default-resources slurm_extra="--qos={self.qos}" '
+            f'--default-resources --slurm-qos {self.qos}" '
             f"slurm_partition={self.workflow_partition} slurm_account={self.account}"
         )