Add script for checking of cluster status

To fix problems with timeouts failing silently.

Taken from snakemake docs.

Also add the required argument to snakemake invocation

run.sh

@@ -7,4 +7,4 @@ module load r/4.0.0
 R CMD BATCH --no-save --no-restore code/simulation-pars.R logs/simulation-pars.Rout
 R CMD BATCH --no-save --no-restore code/method-pars.R logs/method-pars.Rout
 
-snakemake -s Snakefile.py --profile slurm
+snakemake -s Snakefile.py --profile slurm --cluster-status status.py

status.py

+#!/usr/bin/env python
+import subprocess
+import sys
+
+jobid = sys.argv[1]
+
+output = str(subprocess.check_output("sacct -j %s --format State --noheader | head -1 | awk '{print $1}'" % jobid, shell=True).strip())
+
+running_status=["PENDING", "CONFIGURING", "COMPLETING", "RUNNING", "SUSPENDED"]
+if "COMPLETED" in output:
+  print("success")
+elif any(r in output for r in running_status):
+  print("running")
+else:
+  print("failed")
+