cluster-generic-submit-cmd with trailing newlines fail to submit jobs

[ning-y]

cluster-generic-submit-cmd formatted as block scalars with trailing newlines do not work, as it seems that the jobs are not submitted.

These work:

cluster-generic-submit-cmd: qsub -q {resources.queue} -l select=1:ncpus={threads}:mem={resources.mem_mb}mb -l walltime={resources.walltime}
cluster-generic-submit-cmd: >-
  qsub -q {resources.queue} -l select=1:ncpus={threads}:mem={resources.mem_mb}mb -l walltime={resources.walltime}
cluster-generic-submit-cmd: |-
  qsub -q {resources.queue} -l select=1:ncpus={threads}:mem={resources.mem_mb}mb -l walltime={resources.walltime}
cluster-generic-submit-cmd: >-
  qsub \
    -q {resources.queue} \
    -l select=1:ncpus={threads}:mem={resources.mem_mb}mb \
    -l walltime={resources.walltime}

But these do not:

cluster-generic-submit-cmd: >
  qsub -q {resources.queue} -l select=1:ncpus={threads}:mem={resources.mem_mb}mb -l walltime={resources.walltime}
cluster-generic-submit-cmd: |
  qsub -q {resources.queue} -l select=1:ncpus={threads}:mem={resources.mem_mb}mb -l walltime={resources.walltime}

This might be because shell=True parses the trailing newline to separate {submitcmd} from {jobscript}, leading {submitcmd} to be parsed as its own command without {jobscript}.

snakemake-executor-plugin-cluster-generic/snakemake_executor_plugin_cluster_generic/__init__.py

Lines 151 to 161 in ce5fc82

	ext_jobid = (
	subprocess.check_output(
	'{submitcmd} "{jobscript}"'.format(
	submitcmd=submitcmd, jobscript=jobscript
	),
	shell=True,
	env=env,
	)
	.decode()
	.split("\n")
	)