diff --git a/src/ccbr_tools/peek.py b/src/ccbr_tools/peek.py
index 46fade0..212bf31 100755
--- a/src/ccbr_tools/peek.py
+++ b/src/ccbr_tools/peek.py
@@ -79,7 +79,7 @@ def pprint(headlist, data, linelength, fn):
 
 
 def peek(filename, buffer, delim="\t"):
-    pargs()
+    # pargs()
 
     # Getting contents of first line
     try:
diff --git a/src/ccbr_tools/pipeline/hpc.py b/src/ccbr_tools/pipeline/hpc.py
index a2651e9..835f37c 100755
--- a/src/ccbr_tools/pipeline/hpc.py
+++ b/src/ccbr_tools/pipeline/hpc.py
@@ -71,7 +71,7 @@ class Biowulf(Cluster):
     GROUP = "CCBR_Pipeliner"
     PIPELINES_HOME = pathlib.Path("/data/CCBR_Pipeliner/Pipelines")
     TOOLS_HOME = pathlib.Path("/data/CCBR_Pipeliner/Tools")
-    CONDA_ACTIVATE = '. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh" && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311'
+    CONDA_ACTIVATE = ". '/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh' && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311"
 
     def __init__(self):
         super().__init__()
@@ -102,7 +102,7 @@ class FRCE(Cluster):
     GROUP = "nci-frederick-ccbr-pipelines"
     PIPELINES_HOME = pathlib.Path("/mnt/projects/CCBR-Pipelines/pipelines")
     TOOLS_HOME = pathlib.Path("/mnt/projects/CCBR-Pipelines/tools")
-    CONDA_ACTIVATE = '. "/mnt/projects/CCBR-Pipelines/resources/miniconda3/etc/profile.d/conda.sh" && conda activate py311'
+    CONDA_ACTIVATE = ". '/mnt/projects/CCBR-Pipelines/resources/miniconda3/etc/profile.d/conda.sh' && conda activate py311"
 
     def __init__(self):
         super().__init__()
diff --git a/src/ccbr_tools/pipeline/nextflow.py b/src/ccbr_tools/pipeline/nextflow.py
index 9dcef1f..8675780 100755
--- a/src/ccbr_tools/pipeline/nextflow.py
+++ b/src/ccbr_tools/pipeline/nextflow.py
@@ -90,7 +90,9 @@ def run(
     if "-preview" not in args_dict.keys():
         if hpc:
             hpc_modules = hpc.modules["nxf"]
-            preview_command = f'bash -c "module load {hpc_modules} && {hpc.env_vars} && {nextflow_command} -preview"'
+            preview_command = (
+                f'bash -c "module load {hpc_modules} && {nextflow_command} -preview"'
+            )
         else:
             preview_command = nextflow_command + " -preview"
         msg_box("Pipeline Preview", errmsg=preview_command)
diff --git a/src/ccbr_tools/send_email.py b/src/ccbr_tools/send_email.py
index 4bee28d..f797de8 100644
--- a/src/ccbr_tools/send_email.py
+++ b/src/ccbr_tools/send_email.py
@@ -49,5 +49,6 @@ def send_email_msg(
         )
     if debug:
         return msg
-    with smtplib.SMTP("localhost") as server:
-        server.send_message(msg)
+    else:
+        with smtplib.SMTP("localhost") as server:
+            server.send_message(msg)
diff --git a/src/ccbr_tools/shell.py b/src/ccbr_tools/shell.py
index b15822e..5ad8fd6 100755
--- a/src/ccbr_tools/shell.py
+++ b/src/ccbr_tools/shell.py
@@ -28,7 +28,7 @@ def shell_run(command_str, capture_output=True, check=True, shell=True, text=Tru
         '/bin/sh: invalid_command: command not found\n'
     """
     out = subprocess.run(
-        command_str, capture_output=capture_output, shell=shell, text=text, check=check
+        command_str, capture_output=capture_output, check=check, shell=shell, text=text
     )
     if capture_output:
         return_val = concat_newline(out.stdout, out.stderr)
diff --git a/tests/data/templates/submit_slurm.sh b/tests/data/templates/submit_slurm.sh
new file mode 100644
index 0000000..dc9e55f
--- /dev/null
+++ b/tests/data/templates/submit_slurm.sh
@@ -0,0 +1,16 @@
+#!/usr/bin/env bash
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=1g
+#SBATCH --time=1-00:00:00
+#SBATCH --parsable
+#SBATCH -J "CCBR_nxf"
+#SBATCH --mail-type=BEGIN,END,FAIL
+#SBATCH --output "log/slurm_%j.log"
+#SBATCH --error "log/slurm_%j.log"
+
+module load nextflow
+
+export SINGULARITY_CACHEDIR=/gpfs/gsfs10/users/CCBR_Pipeliner/Tools/ccbr_tools/tools-dev-sovacool/.singularity
+if ! command -v spooker 2>&1 >/dev/null; then export PATH="$PATH:/data/CCBR_Pipeliner/Tools/ccbr_tools/v0.2/bin/"; fi
+
+nextflow run main.nf -stub
diff --git a/tests/test_cli.py b/tests/test_cli.py
index f58ec2c..a3171ba 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -2,15 +2,23 @@
 
 import os
 import pathlib
+import pytest
 import tempfile
 
+is_ci = (
+    os.environ.get("CI", "false") == "true"
+)  # Set CI to false if not in a CI environment
+
 
 def test_version_flag():
-    assert shell_run("ccbr_tools -v").startswith("ccbr_tools, version ")
+    version = shell_run("ccbr_tools --version")
+    assert version.startswith("ccbr_tools, version ")
 
 
+@pytest.mark.skipif(is_ci, reason="Skip on CI")
 def test_version_cmd():
-    assert shell_run("ccbr_tools version --debug").startswith("VERSION file path")
+    version = shell_run("ccbr_tools version --debug")
+    assert version.startswith("VERSION file path")
 
 
 def test_help():
@@ -52,6 +60,7 @@ def test_help_peek():
     assert "USAGE: peek <file.tsv> [buffer]" in shell_run("peek -h")
 
 
+@pytest.mark.skipif(is_ci, reason="Skip on CI")
 def test_send_email():
     assert "" == shell_run("ccbr_tools send-email -d")
 
@@ -79,7 +88,7 @@ def test_install():
     output = shell_run("ccbr_tools install champagne v0.3.0 --hpc biowulf", check=False)
     assert (
         output
-        == """. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh" && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311
+        == """. '/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh' && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311
 pip install git+https://github.com/CCBR/CHAMPAGNE.git@v0.3.0 -t /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0
 chmod -R a+rX /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0
 chown -R :CCBR_Pipeliner /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0
diff --git a/tests/test_nextflow.py b/tests/test_nextflow.py
index bddfc6b..1a7389a 100644
--- a/tests/test_nextflow.py
+++ b/tests/test_nextflow.py
@@ -3,7 +3,7 @@
 import tempfile
 
 from ccbr_tools.pipeline.nextflow import run, init
-from ccbr_tools.pipeline.hpc import Biowulf, FRCE
+from ccbr_tools.pipeline.hpc import Biowulf, FRCE, get_hpc
 from ccbr_tools.shell import exec_in_context
 
 
diff --git a/tests/test_pipeline_hpc.py b/tests/test_pipeline_hpc.py
index d2a34a8..3c4ee42 100644
--- a/tests/test_pipeline_hpc.py
+++ b/tests/test_pipeline_hpc.py
@@ -12,7 +12,7 @@ def test_hpc_biowulf():
                 "<class 'ccbr_tools.pipeline.hpc.Biowulf'>({'name': 'biowulf'"
             ),
             hpc.CONDA_ACTIVATE
-            == '. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh" && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311',
+            == ". '/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh' && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311",
         ]
     )
 
@@ -26,7 +26,7 @@ def test_hpc_frce():
             "/mnt/projects/CCBR-Pipelines/bin" in hpc.env_vars,
             hpc.singularity_sif_dir == "/mnt/projects/CCBR-Pipelines/SIFs",
             hpc.CONDA_ACTIVATE
-            == '. "/mnt/projects/CCBR-Pipelines/resources/miniconda3/etc/profile.d/conda.sh" && conda activate py311',
+            == ". '/mnt/projects/CCBR-Pipelines/resources/miniconda3/etc/profile.d/conda.sh' && conda activate py311",
         ]
     )
 
diff --git a/tests/test_software.py b/tests/test_software.py
index 6077fb1..b758d7c 100644
--- a/tests/test_software.py
+++ b/tests/test_software.py
@@ -44,7 +44,7 @@ def test_install():
     )
     assert (
         result
-        == """. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh" && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311
+        == """. '/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh' && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311
 pip install git+https://github.com/CCBR/CHAMPAGNE.git@v0.3.0 -t /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0
 chmod -R a+rX /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0
 chown -R :CCBR_Pipeliner /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0
@@ -67,7 +67,7 @@ def test_install_dev():
     )
     assert (
         result
-        == """. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh" && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311
+        == """. '/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh' && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311
 pip install git+https://github.com/CCBR/CHAMPAGNE.git@main -t /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0-dev
 chmod -R a+rX /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0-dev
 chown -R :CCBR_Pipeliner /data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/.v0.3.0-dev
@@ -86,7 +86,7 @@ def test_custom():
     )
     assert (
         result
-        == """. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh" && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311
+        == """. '/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh' && conda activate /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311
 pip install git+https://github.com/CCBR/cooltool.git@v1.0.0 -t /data/CCBR_Pipeliner/Tools/cooltool/.v1.0.0
 chmod -R a+rX /data/CCBR_Pipeliner/Tools/cooltool/.v1.0.0
 chown -R :CCBR_Pipeliner /data/CCBR_Pipeliner/Tools/cooltool/.v1.0.0
diff --git a/tests/test_templates.py b/tests/test_templates.py
index 97639e4..2af7ae9 100644
--- a/tests/test_templates.py
+++ b/tests/test_templates.py
@@ -4,6 +4,7 @@
 import tempfile
 
 from ccbr_tools.templates import read_template, use_template, use_quarto_ext
+from ccbr_tools.pipeline.hpc import get_hpc
 
 
 def test_read_template():
@@ -38,6 +39,18 @@ def test_use_template():
     assert all(assertions)
 
 
+def generate_slurm_template():
+    hpc = get_hpc(debug="biowulf")
+    use_template(
+        "submit_slurm.sh",
+        output_filepath="tests/data/templates/submit_slurm.sh",
+        PIPELINE="CCBR_nxf",
+        MODULES=hpc.modules["nxf"],
+        ENV_VARS=hpc.env_vars,
+        RUN_COMMAND="nextflow run main.nf -stub",
+    )
+
+
 def test_use_template_blanks():
     with tempfile.TemporaryDirectory() as tmp_dir:
         out_filepath = pathlib.Path(tmp_dir) / "test.sh"