refactor: simplify templates

src/ccbr_tools/pipeline/cache.py

@@ -3,11 +3,13 @@
 import sys
 
 
-def get_singularity_cachedir(output_dir, cache_dir=None):
+def get_singularity_cachedir(output_dir=None, cache_dir=None):
     """Returns the singularity cache directory.
     If no user-provided cache directory is provided,
     the default singularity cache is in the output directory.
     """
+    if not output_dir:
+        output_dir = os.getcwd()
     if not cache_dir:
         cache_dir = os.path.join(output_dir, ".singularity")
     return cache_dir

src/ccbr_tools/pipeline/hpc.py

@@ -1,13 +1,19 @@
 from .util import get_hpcname
+from .cache import get_singularity_cachedir
 
 
 class Cluster:
     def __init__(self):
         self.name = None
-        self.slurm_script = {"nxf": None, "smk": None}
         self.modules = {"nxf": None, "smk": None}
+        self.env_vars = "\n".join(
+            (f"export SINGULARITY_CACHEDIR={get_singularity_cachedir()}",)
+        )
         self.singularity_sif_dir = None
 
+    def __repr__(self):
+        return f"{self.__class__}({self.__dict__})"
+
     def __bool__(self):
         return bool(self.name)
 
@@ -18,10 +24,6 @@ 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",
@@ -33,9 +35,14 @@ 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"
+        self.env_vars = "\n".join(
+            (
+                self.env_vars,
+                f"export PATH=${{PATH}}:/mnt/projects/CCBR-Pipelines/bin",
+            )
+        )
 
 
 def get_hpc(debug=False):

src/ccbr_tools/pipeline/nextflow.py

@@ -11,6 +11,7 @@
 from ..pkg_util import msg_box, use_template
 from ..shell import shell_run
 from .hpc import get_hpc
+from .cache import get_singularity_cachedir
 
 
 def run(
@@ -72,18 +73,17 @@ def run(
     if mode == "slurm":
         slurm_filename = "submit_slurm.sh"
         use_template(
-            hpc.slurm_script["nxf"],
-            output_filepath=slurm_filename,
+            "submit_slurm.sh",
             PIPELINE=pipeline_name if pipeline_name else "CCBR_nxf",
+            MODULES=hpc.modules,
+            ENV_VARS=hpc.env_vars,
             RUN_COMMAND=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 {hpc.modules} && {nextflow_command}"'
-            )
+            nextflow_command = f'bash -c "module load {hpc.modules} && {hpc.env_vars} && {nextflow_command}"'
         run_command = nextflow_command
     else:
         raise ValueError(f"mode {mode} not recognized")

src/ccbr_tools/pkg_util.py

@@ -174,7 +174,7 @@ def read_template(template_name):
 
 def use_template(template_name, output_filepath=None, **kwargs):
     """
-    Uses a template, formats variables, and write it to a file.
+    Uses a template, formats variables, and writes it to a file.
     Args:
         template_name (str): The name of the template to use.
         output_filepath (str, optional): The filepath to save the output file. If not provided, it will be written to `template_name` in the current working directory.

src/ccbr_tools/templates/slurm_smk_biowulf.sh → src/ccbr_tools/templates/submit_slurm.sh

@@ -8,6 +8,8 @@
 #SBATCH --output "log/slurm_%j.log"
 #SBATCH --output "log/slurm_%j.log"
 
-module load ccbrpipeliner snakemake/7 singularity
+module load {MODULES}
+
+{ENV_VARS}
 
 {RUN_COMMAND}

tests/test_hpc.py

@@ -7,8 +7,6 @@ def test_hpc_biowulf():
         [
             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",
         ]
     )
@@ -20,13 +18,12 @@ def test_hpc_frce():
         [
             hpc,
             hpc.name == "frce",
-            hpc.slurm_script
-            == {"nxf": "slurm_nxf_frce.sh", "smk": "slurm_smk_frce.sh"},
+            "/mnt/projects/CCBR-Pipelines/bin" in hpc.env_vars,
             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])
+    assert not any([hpc, hpc.name, *hpc.modules.values(), hpc.singularity_sif_dir])

tests/test_pkg_util.py

@@ -2,7 +2,7 @@
 
 
 def test_read_template():
-    template_str = read_template("slurm_nxf_biowulf.sh")
+    template_str = read_template("submit_slurm.sh")
     assert all(
         [
             template_str.startswith("#!/usr/bin/env bash"),