diff --git a/.github/workflows/test_pipelines.yml b/.github/workflows/test_pipelines.yml
index cd692568..3de19bfe 100755
--- a/.github/workflows/test_pipelines.yml
+++ b/.github/workflows/test_pipelines.yml
@@ -49,11 +49,11 @@ jobs:
     - name: Test design works
       shell: pwsh
       run: |
-        seqnado-design chip tests/data/fastq/CTCF*.fastq.gz
-    - name: Test with pytest
+        seqnado-design chip tests/data/fastq/chip-rx*.fastq.gz
+    - name: Test pipeline
       shell: pwsh
       run: |
-        pytest -vv -s --cov=./ --cov-report=xml --cores 4
+        pytest -vv -s --cov=./ --cov-report=xml --cores 4 
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v4.0.1
       with:
diff --git a/.gitignore b/.gitignore
index c650a40f..5281b1c2 100755
--- a/.gitignore
+++ b/.gitignore
@@ -18,3 +18,4 @@ fastq_class_sandbox.ipynb
 test_rna_size_factors.ipynb
 tests/data/*
 pytestdebug.log
+sps*
diff --git a/tests/test_pipelines.py b/tests/test_pipelines.py
index 46f7c757..7e439845 100755
--- a/tests/test_pipelines.py
+++ b/tests/test_pipelines.py
@@ -248,7 +248,8 @@ def user_inputs(
         "pileup_method": "deeptools",
         "scale": "no",
         "make_heatmaps": "no",
-        "call_peaks": "no",
+        "call_peaks": "yes",
+        "peak_calling_method": "lanceotron",
     }
 
     defaults_rna = {
@@ -336,7 +337,7 @@ def config_yaml_for_testing(config_yaml, assay):
 
     if assay == "chip":
         config["pileup_method"] = ["deeptools", "homer"]
-        config["peak_calling_method"] = ["lanceotron", "macs", "homer"]
+        config["peak_calling_method"] = ["lanceotron"]
         config["library_complexity"] = False
         config["bowtie2"]["options"] = "--no-mixed --no-discordant"
     elif assay == "chip-rx":
@@ -344,7 +345,7 @@ def config_yaml_for_testing(config_yaml, assay):
         config["peak_calling_method"] = ["seacr"]
     elif assay == "atac":
         config["call_peaks"] = True
-        config["peak_calling_method"] = ["macs"]
+        config["peak_calling_method"] = ["lanceotron", "macs", "homer"]
 
     with open(config_yaml, "w") as f:
         yaml.dump(config, f)