diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index bb07bfe5..f2bad8fa 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -48,7 +48,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        tests: ["test_bins", "test_coassembly", "test_model_information", "test_mouse_all_pep_lengths", "test_bins_only"] # add further test profiles here, will be run in parallel (but only with one nextflow version)
+        tests: ["test_bins", "test_coassembly", "test_model_information", "test_mouse_all_pep_lengths", "test_bins_only", "test_mhcflurry", "test_mhcnuggets_1", "test_mhcnuggets_2"] # add further test profiles here, will be run in parallel (but only with one nextflow version)
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
diff --git a/conf/test_mhcflurry.config b/conf/test_mhcflurry.config
new file mode 100644
index 00000000..a99b8c9f
--- /dev/null
+++ b/conf/test_mhcflurry.config
@@ -0,0 +1,23 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/metapep -profile test_assembly_only,<docker/singularity>
+ */
+
+params {
+    config_profile_name = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus = 2
+    max_memory = 6.GB
+    max_time = 48.h
+
+    // Input data
+    input = "https://github.com/nf-core/test-datasets/raw/metapep/samplesheets/input.assembly_only.csv"
+
+    // Change prediction method
+    pred_method = 'mhcflurry'
+}
diff --git a/conf/test_mhcnuggets_1.config b/conf/test_mhcnuggets_1.config
new file mode 100644
index 00000000..fd2edba2
--- /dev/null
+++ b/conf/test_mhcnuggets_1.config
@@ -0,0 +1,23 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/metapep -profile test_assembly_only,<docker/singularity>
+ */
+
+params {
+    config_profile_name = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus = 2
+    max_memory = 6.GB
+    max_time = 48.h
+
+    // Input data
+    input = "https://github.com/nf-core/test-datasets/raw/metapep/samplesheets/input.assembly_only.csv"
+
+    // Change prediction method
+    pred_method = 'mhcnuggets-class-1'
+}
diff --git a/conf/test_mhcnuggets_2.config b/conf/test_mhcnuggets_2.config
new file mode 100644
index 00000000..8c5f3650
--- /dev/null
+++ b/conf/test_mhcnuggets_2.config
@@ -0,0 +1,23 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/metapep -profile test_assembly_only,<docker/singularity>
+ */
+
+params {
+    config_profile_name = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus = 2
+    max_memory = 6.GB
+    max_time = 48.h
+
+    // Input data
+    input = "https://github.com/nf-core/test-datasets/raw/metapep/samplesheets/input.assembly_only.csv"
+
+    // Change prediction method
+    pred_method = 'mhcnuggets-class-2'
+}
diff --git a/nextflow.config b/nextflow.config
index 861e2819..560fb54e 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -195,6 +195,9 @@ profiles {
     test_full                   { includeConfig 'conf/test_full.config'                     }
     test_model_information      { includeConfig 'conf/test_model_information.config'        }
     test_mouse_all_pep_lengths  { includeConfig 'conf/test_mouse_all_pep_lengths.config'    }
+    test_mhcflurry              { includeConfig 'conf/test_mhcflurry.config'                }
+    test_mhcnuggets_1           { includeConfig 'conf/test_mhcnuggets_1.config'             }
+    test_mhcnuggets_2           { includeConfig 'conf/test_mhcnuggets_2.config'             }
 }
 
 // Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile