refactor: create classes for HPC options

src/ccbr_tools/pipeline/hpc.py

@@ -0,0 +1,44 @@
+from .util import get_hpcname
+
+
+class Cluster:
+    def __init__(self):
+        self.name = None
+        self.slurm_script = {"nxf": None, "smk": None}
+        self.modules = {"nxf": None, "smk": None}
+        self.singularity_sif_dir = None
+
+    def __bool__(self):
+        return bool(self.name)
+
+    __nonzero__ = __bool__
+
+
+class Biowulf(Cluster):
+    def __init__(self):
+        super().__init__()
+        self.name = "biowulf"
+        self.slurm_script = {
+            "nxf": "slurm_nxf_biowulf.sh",
+            "smk": "slurm_smk_biowulf.sh",
+        }
+        self.modules = {
+            "nxf": "ccbrpipeliner nextflow",
+            "smk": "ccbrpipeliner snakemake/7 singularity",
+        }
+        self.singularity_sif_dir = "/data/CCBR_Pipeliner/SIFs"
+
+
+class FRCE(Cluster):
+    def __init__(self):
+        super().__init__()
+        self.name = "frce"
+        self.slurm_script = {"nxf": "slurm_nxf_frce.sh", "smk": "slurm_smk_frce.sh"}
+        self.modules = {"nxf": "nextflow", "smk": "snakemake/7 singularity"}
+        self.singularity_sif_dir = "/mnt/projects/CCBR-Pipelines/SIFs"
+
+
+def get_hpc(debug=False):
+    hpc_options = {"biowulf": Biowulf, "frce": FRCE}
+    hpc_name = get_hpcname() if not debug else debug
+    return hpc_options.get(hpc_name, Cluster)()

src/ccbr_tools/pipeline/nextflow.py

@@ -8,31 +8,24 @@
     Run a Nextflow workflow.
 """
 
-from ..pkg_util import repo_base, msg_box, use_template
+from ..pkg_util import msg_box, use_template
 from ..shell import shell_run
-from .util import get_hpcname
+from .hpc import get_hpc
 
 
 def run(
-    nextfile_path=None,
-    nextflow_args=None,
+    nextfile_path,
+    nextflow_args=[],
     mode="local",
     pipeline_name=None,
     debug=False,
-    hpc_options={
-        "biowulf": {"profile": "biowulf", "slurm": "slurm_nxf_biowulf.sh"},
-        "fnlcr": {
-            "profile": "frce",
-            "slurm": "slurm_nxf_frce.sh",
-        },
-    },
 ):
     """
     Run a Nextflow workflow
 
     Args:
-        nextfile_path (str, optional): Path to the Nextflow file. Defaults to None.
-        nextflow_args (list, optional): Additional Nextflow arguments. Defaults to None.
+        nextfile_path (str, optional): Path to the Nextflow file.
+        nextflow_args (list, optional): Additional Nextflow arguments. Defaults to an empty list.
         mode (str, optional): Execution mode. Defaults to "local".
         hpc_options (dict, optional): HPC options. Defaults to {"biowulf": {"profile": "biowulf", "slurm": "assets/slurm_header_biowulf.sh"}, "fnlcr": {"profile": "frce", "slurm": "assets/slurm_header_frce.sh"}}.
 
@@ -44,7 +37,7 @@ def run(
     """
     nextflow_command = ["nextflow", "run", nextfile_path]
 
-    hpc = get_hpcname()
+    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
@@ -65,7 +58,7 @@ def run(
     if mode == "slurm":
         profiles.add("slurm")
     if hpc:
-        profiles.add(hpc_options[hpc]["profile"])
+        profiles.add(hpc.name)
     if (
         profiles
     ):  # only add to the profiles if there are any. there are none when champagne is run on GitHub Actions.
@@ -79,23 +72,22 @@ def run(
     if mode == "slurm":
         slurm_filename = "submit_slurm.sh"
         use_template(
-            hpc_options[hpc]["slurm"],
-            output_filepath="submit_slurm.sh",
+            hpc.slurm_script["nxf"],
+            output_filepath=slurm_filename,
             PIPELINE=pipeline_name if pipeline_name else "CCBR_nxf",
             RUN_COMMAND=nextflow_command,
         )
-        with open(slurm_filename, "w") as sbatch_file:
-            with open(repo_base(hpc_options[hpc]["slurm"]), "r") as template:
-                sbatch_file.writelines(template.readlines())
-            sbatch_file.write(nextflow_command)
         run_command = f"sbatch {slurm_filename}"
         msg_box("Slurm batch job", errmsg=run_command)
     elif mode == "local":
         if hpc:
-            nextflow_command = f'bash -c "module load nextflow && {nextflow_command}"'
+            nextflow_command = (
+                f'bash -c "module load {hpc.modules} && {nextflow_command}"'
+            )
         run_command = nextflow_command
     else:
         raise ValueError(f"mode {mode} not recognized")
 
     # Run Nextflow
-    shell_run(run_command, capture_output=False)
+    if not debug:
+        shell_run(run_command, capture_output=False)

tests/test_hpc.py

@@ -0,0 +1,32 @@
+from ccbr_tools.pipeline.hpc import get_hpc
+
+
+def test_hpc_biowulf():
+    hpc = get_hpc(debug="biowulf")
+    assert all(
+        [
+            hpc,
+            hpc.name == "biowulf",
+            hpc.slurm_script
+            == {"nxf": "slurm_nxf_biowulf.sh", "smk": "slurm_smk_biowulf.sh"},
+            hpc.singularity_sif_dir == "/data/CCBR_Pipeliner/SIFs",
+        ]
+    )
+
+
+def test_hpc_frce():
+    hpc = get_hpc(debug="frce")
+    assert all(
+        [
+            hpc,
+            hpc.name == "frce",
+            hpc.slurm_script
+            == {"nxf": "slurm_nxf_frce.sh", "smk": "slurm_smk_frce.sh"},
+            hpc.singularity_sif_dir == "/mnt/projects/CCBR-Pipelines/SIFs",
+        ]
+    )
+
+
+def test_hpc_none():
+    hpc = get_hpc(debug="")
+    assert not any([hpc, hpc.name, *hpc.slurm_script.values(), hpc.singularity_sif_dir])

tests/test_nextflow.py

@@ -0,0 +1,8 @@
+from ccbr_tools.pipeline.nextflow import run
+from ccbr_tools.shell import exec_in_context
+
+
+def test_nextflow_basic():
+    assert "nextflow run CCBR/CHAMPAGNE" in exec_in_context(
+        run, "CCBR/CHAMPAGNE", debug=True
+    )