diff --git a/illqclib/main.py b/illqclib/main.py
index e8503bf..396d282 100644
--- a/illqclib/main.py
+++ b/illqclib/main.py
@@ -67,7 +67,7 @@ class Trimmomatic(object):
             "ILLUMINACLIP:%s:2:30:10:8:true" % self._adapter_fp,
             "LEADING:%d" % self.config["leading"],
             "TRAILING:%d" % self.config["trailing"],
-            "SLIDINGWINDOW:%d:%d" % self.config["slidingwindow"],
+            "SLIDINGWINDOW:%d:%d" % tuple(self.config["slidingwindow"]),
             "MINLEN:%d" % self.config["minlen"],
             ]
 

Cannot configure setting for sliding window
Python needs a tuple value for this setting, but JSON does not support tuple types.  Suggest converting to value tuple before line 70:

https://github.com/PennChopMicrobiomeProgram/illqc/blob/master/illqclib/main.py#L70
diff --git a/test/test_main.py b/test/test_main.py
index 7a75113..803ed7b 100644
--- a/test/test_main.py
+++ b/test/test_main.py
@@ -26,17 +26,19 @@ class ConfigTests(unittest.TestCase):
 
 
 class TrimmomaticTests(unittest.TestCase):
+    config_vals = {
+        "trimmomatic_jar_fp": "trimmomatic-0.30.jar",
+        "adapter_dir": "adapters",
+        "adapter": "NexteraPE-PE",
+        "leading": 3,
+        "trailing": 3,
+        "slidingwindow": (4, 15),
+        "minlen": 36,
+        "java_heapsize":"200M"
+    }
+
     def test_make_command(self):
-        app = Trimmomatic({
-            "trimmomatic_jar_fp": "trimmomatic-0.30.jar",
-            "adapter_dir": "adapters",
-            "adapter": "NexteraPE-PE",
-            "leading": 3,
-            "trailing": 3,
-            "slidingwindow": (4, 15),
-            "minlen": 36,
-	    "java_heapsize":"200M"
-            })
+        app = Trimmomatic(self.config_vals)
         observed = app.make_command("a.fastq", "b.fastq", "mydir")
         expected = [
             'java', '-Xmx200M', '-jar', 'trimmomatic-0.30.jar', 'PE', '-phred33',
@@ -47,3 +49,18 @@ class TrimmomaticTests(unittest.TestCase):
             'LEADING:3', 'TRAILING:3', 'SLIDINGWINDOW:4:15', 'MINLEN:36',
             ]
         self.assertEqual(observed, expected)
+
+    def test_make_command_sliding_window_as_list(self):
+        config_vals = self.config_vals.copy()
+        config_vals["slidingwindow"] = [6, 32]
+        app = Trimmomatic(config_vals)
+        observed = app.make_command("a.fastq", "b.fastq", "mydir")
+        expected = [
+            'java', '-Xmx200M', '-jar', 'trimmomatic-0.30.jar', 'PE', '-phred33',
+            'a.fastq', 'b.fastq',
+            'mydir/a.fastq', 'mydir/a_unpaired.fastq',
+            'mydir/b.fastq', 'mydir/b_unpaired.fastq',
+            'ILLUMINACLIP:adapters/NexteraPE-PE.fa:2:30:10:8:true',
+            'LEADING:3', 'TRAILING:3', 'SLIDINGWINDOW:6:32', 'MINLEN:36',
+            ]
+        self.assertEqual(observed, expected)

pip install -e .[dev]
parse_log_pytest
requirements.txt
pytest pytest-cov pytest-xdist pytest-mock pytest-asyncio numpy>=1.16.0 pandas>=1.0.0
apt-get update apt-get install -y gcc
3.9
pytest --no-header -rA --tb=line --color=no -p no:cacheprovider -W ignore::DeprecationWarning
coverage==7.8.0
exceptiongroup==1.2.2
execnet==2.1.1
-e git+https://github.com/PennChopMicrobiomeProgram/illqc.git@bc504d4c93300db446ab7b70cb0660f682d07687#egg=illQC
iniconfig==2.1.0
numpy==2.0.2
packaging==24.2
pandas==2.2.3
pluggy==1.5.0
pytest==8.3.5
pytest-asyncio==0.26.0
pytest-cov==6.0.0
pytest-mock==3.14.0
pytest-xdist==3.6.1
python-dateutil==2.9.0.post0
pytz==2025.2
six==1.17.0
tomli==2.2.1
typing_extensions==4.13.0
tzdata==2025.2

name: illqc
channels:
  - defaults
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/r
  - conda-forge
dependencies:
  - _libgcc_mutex=0.1=main
  - _openmp_mutex=5.1=1_gnu
  - ca-certificates=2025.2.25=h06a4308_0
  - ld_impl_linux-64=2.40=h12ee557_0
  - libffi=3.4.4=h6a678d5_1
  - libgcc-ng=11.2.0=h1234567_1
  - libgomp=11.2.0=h1234567_1
  - libstdcxx-ng=11.2.0=h1234567_1
  - ncurses=6.4=h6a678d5_0
  - openssl=3.0.16=h5eee18b_0
  - pip=25.0=py39h06a4308_0
  - python=3.9.21=he870216_1
  - readline=8.2=h5eee18b_0
  - setuptools=75.8.0=py39h06a4308_0
  - sqlite=3.45.3=h5eee18b_0
  - tk=8.6.14=h39e8969_0
  - wheel=0.45.1=py39h06a4308_0
  - xz=5.6.4=h5eee18b_1
  - zlib=1.2.13=h5eee18b_1
  - pip:
      - coverage==7.8.0
      - exceptiongroup==1.2.2
      - execnet==2.1.1
      - iniconfig==2.1.0
      - numpy==2.0.2
      - packaging==24.2
      - pandas==2.2.3
      - pluggy==1.5.0
      - pytest==8.3.5
      - pytest-asyncio==0.26.0
      - pytest-cov==6.0.0
      - pytest-mock==3.14.0
      - pytest-xdist==3.6.1
      - python-dateutil==2.9.0.post0
      - pytz==2025.2
      - six==1.17.0
      - tomli==2.2.1
      - typing-extensions==4.13.0
      - tzdata==2025.2
prefix: /opt/conda/envs/illqc

test/test_main.py::TrimmomaticTests::test_make_command_sliding_window_as_list
test/test_main.py::ConfigTests::test_default_config_locataion test/test_main.py::TrimmomaticTests::test_make_command
illqclib/main.py
illqclib/main.py