test: slurm mode

src/ccbr_tools/pipeline/nextflow.py

@@ -19,6 +19,7 @@ def run(
     mode="local",
     pipeline_name=None,
     debug=False,
+    hpc=get_hpc(),
 ):
     """
     Run a Nextflow workflow
@@ -33,7 +34,6 @@ def run(
     """
     nextflow_command = ["nextflow", "run", nextfile_path]
 
-    hpc = get_hpc()
     if mode == "slurm" and not hpc:
         raise ValueError("mode is 'slurm' but no HPC environment was detected")
     # add any additional Nextflow commands

tests/test_nextflow.py

@@ -1,15 +1,33 @@
 from ccbr_tools.pipeline.nextflow import run
-from ccbr_tools.pipeline.hpc import get_hpc
+from ccbr_tools.pipeline.hpc import get_hpc, Biowulf, FRCE
 from ccbr_tools.shell import exec_in_context
 
+import tempfile
+
 
 def test_nextflow_basic():
     output = exec_in_context(run, "CCBR/CHAMPAGNE", debug=True)
     assert "nextflow run CCBR/CHAMPAGNE" in output
 
 
 def test_nextflow_hpc():
-    hpc = get_hpc()
-    if hpc.name == "biowulf" or hpc.name == "frce":
-        output = exec_in_context(run, "CCBR/CHAMPAGNE", debug=True)
-        assert "module load" in output
+    assert all(
+        [
+            "module load"
+            in exec_in_context(run, "CCBR/CHAMPAGNE", debug=True, hpc=Biowulf()),
+            "module load"
+            in exec_in_context(run, "CCBR/CHAMPAGNE", debug=True, hpc=FRCE()),
+        ]
+    )
+
+
+def test_nextflow_slurm():
+    assert "sbatch submit_slurm.sh" in exec_in_context(
+        run, "CCBR/CHAMPAGNE", debug=True, hpc=Biowulf(), mode="slurm"
+    )
+
+
+if __name__ == "__main__":
+    print(
+        exec_in_context(run, "CCBR/CHAMPAGNE", debug=True, hpc=Biowulf(), mode="slurm")
+    )