Merge branch 'main' into feat/requeue-flag

pyproject.toml

@@ -25,7 +25,7 @@ black = "^23.7.0"
 flake8 = "^6.1.0"
 coverage = "^7.3.1"
 pytest = "^7.4.2"
-snakemake = {git = "https://github.com/snakemake/snakemake.git"}
+snakemake = "^8.20.0"
 
 [tool.coverage.run]
 omit = [".*", "*/site-packages/*", "Snakefile"]

snakemake_executor_plugin_slurm/__init__.py

@@ -149,7 +149,7 @@ def run_job(self, job: JobExecutorInterface):
             f"sbatch "
             f"--parsable "
             f"--job-name {self.run_uuid} "
-            f"--output {slurm_logfile} "
+            f"--output '{slurm_logfile}' "
             f"--export=ALL "
             f"--comment {comment_str}"
         )
@@ -423,6 +423,14 @@ def cancel_jobs(self, active_jobs: List[SubmittedJobInfo]):
                 )
             except subprocess.TimeoutExpired:
                 self.logger.warning("Unable to cancel jobs within a minute.")
+            except subprocess.CalledProcessError as e:
+                msg = e.stderr.strip()
+                if msg:
+                    msg = f": {msg}"
+                raise WorkflowError(
+                    "Unable to cancel jobs with scancel "
+                    f"(exit code {e.returncode}){msg}"
+                ) from e
 
     async def job_stati(self, command):
         """Obtain SLURM job status of all submitted jobs with sacct