Merge pull request #47 from mbhall88/hotfix/#45

Support quoted jobid from snakemake v7.1.1

CHANGELOG.md

@@ -18,6 +18,10 @@ This document tracks changes to the `master` branch of the profile.
 
 - Default project and queue will be removed from the submission command if they are present in the `lsf.yaml`
 
+### Fixed
+
+- Support quoted jobid from `snakemake>=v7.1.1` [[#45][45]]
+
 ## [0.1.2] - 01/04/2021
 
 ### Added
@@ -83,6 +87,7 @@ This document tracks changes to the `master` branch of the profile.
 [9]: https://github.com/Snakemake-Profiles/lsf/pull/9
 [36]: https://github.com/Snakemake-Profiles/lsf/issues/36
 [39]: https://github.com/Snakemake-Profiles/lsf/issues/39
+[45]: https://github.com/Snakemake-Profiles/lsf/issues/45
 [0.1.0]: https://github.com/Snakemake-Profiles/lsf/releases/tag/0.1.0
 [0.1.1]: https://github.com/Snakemake-Profiles/lsf/releases/tag/0.1.1
 [0.1.2]: https://github.com/Snakemake-Profiles/lsf/releases/tag/0.1.2

{{cookiecutter.profile_name}}/lsf_status.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
 
+import shlex
 import sys
 import time
 from pathlib import Path
@@ -198,8 +199,12 @@ def get_status(self) -> str:
 
 
 if __name__ == "__main__":
-    jobid = int(sys.argv[1])
-    outlog = sys.argv[2]
+    # need to support quoted and unquoted jobid
+    # see https://github.com/Snakemake-Profiles/lsf/issues/45
+    split_args = shlex.split(" ".join(sys.argv[1:]))
+    jobid = int(split_args[0])
+    outlog = split_args[1]
+
     if CookieCutter.get_unknwn_behaviour().lower() == "wait":
         kill_unknown = False
     elif CookieCutter.get_unknwn_behaviour().lower() == "kill":