diff --git a/janis_assistant/engines/cromwell/cromwellconfiguration.py b/janis_assistant/engines/cromwell/cromwellconfiguration.py index 63df34b..597f2c6 100644 --- a/janis_assistant/engines/cromwell/cromwellconfiguration.py +++ b/janis_assistant/engines/cromwell/cromwellconfiguration.py @@ -358,7 +358,7 @@ def slurm( afternotokaycommand = "" if afternotokaycatch: - afternotokaycommand = f" && NTOKDEP=$({sbatch} --parsable --job-name \"catch-$jobname\" --kill-on-invalid-dep=yes {partition_string} --time '0:60' --dependency=afternotokay:$JOBID --wrap '{CromwellConfiguration.CATCH_ERROR_COMMAND}')" + afternotokaycommand = f" && NTOKDEP=$({sbatch} --parsable --job-name \"catch-$jobname\" --kill-on-invalid-dep=yes {partition_string} --time '0:60' --dependency=afternotok:$JOBID --wrap '{CromwellConfiguration.CATCH_ERROR_COMMAND}')" return cls( actor_factory="cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory", @@ -433,7 +433,7 @@ def slurm_singularity( afternotokaycommand = "" if afternotokaycatch: - afternotokaycommand = f" && NTOKDEP=$({sbatch} --parsable --job-name \"catch-$jobname\" --kill-on-invalid-dep=yes {partition_string} --time '0:60' --dependency=afternotokay:$JOBID --wrap '{CromwellConfiguration.CATCH_ERROR_COMMAND}')" + afternotokaycommand = f" && NTOKDEP=$({sbatch} --parsable --job-name \"catch-$jobname\" --kill-on-invalid-dep=yes {partition_string} --time '0:60' --dependency=afternotok:$JOBID --wrap '{CromwellConfiguration.CATCH_ERROR_COMMAND}')" emailextra = ( f'--mail-user "{jobemail}" --mail-type END' if jobemail else ""