Merge pull request #83 from Snakemake-Profiles/resources-partition

Test resources partition key

README.md

@@ -170,7 +170,16 @@ Resources specified in Snakefiles must all be in the correct
 unit/format as expected by `sbatch`. The implemented resource names
 are given (and may be adjusted) in the `slurm_utils.RESOURCE_MAPPING`
 global. This is intended for system agnostic resources such as time
-and memory.
+and memory. Currently supported resources are `time`, `mem`,
+`mem-per-cpu`, `nodes`, and `partition`. An example rule resources
+configuration follows:
+
+    rule bwa_mem:
+        resources:
+            time = "00:10:00",
+            mem = 12000,
+            partition = "debug"
+
 
 ### Advanced argument conversion (EXPERIMENTAL)
 By default, Snakefile resources are provided as-is to the sbatch

tests/Snakefile

@@ -77,3 +77,16 @@ rule wildcard_job:
 rule simemory:
     output: "siunit.txt"
     shell: "touch {output}"
+
+
+rule set_partition_in_cc:
+    output: "partition.cc.txt"
+    shell:
+        "echo {resources} > {output}"
+
+rule set_partition_in_resources:
+    output: "partition.resources.txt"
+    resources:
+        partition = "debug"
+    shell:
+        "echo {resources} > {output}"

tests/cluster-config.yaml

@@ -9,3 +9,6 @@ short_queue:
 
 simemory:
   mem: 1G
+
+set_partition_in_cc:
+  partition: debug

tests/test_slurm.py

@@ -99,3 +99,11 @@ def test_si_units(smk_runner, profile):
     )
     assert "Memory specification can not be satisfied" in smk_runner.output
     assert "--mem=1000" in smk_runner.output
+
+
+@pytest.mark.parametrize("cluster_config", [True, False])
+def test_partition(smk_runner, profile, cluster_config):
+    options = f"--cluster-config {smk_runner.cluster_config}" if cluster_config else ""
+    target = "partition.cc.txt" if cluster_config else "partition.resources.txt"
+    smk_runner.make_target(target, options=options, stream=False)
+    assert smk_runner.check_jobstatus("debug", "-n -o Partition")