nf-core · MaximilianStammnitz · Feb 16, 2026 · Feb 12, 2026
diff --git a/conf/test.config b/conf/test.config
@@ -23,8 +23,11 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input  = params.pipelines_testdata_base_path + 'samplesheet_qc_only.csv'// Genome references
-    genome = 'R64-1-1'
+    input = params.pipelines_testdata_base_path + 'deepmutscan/samplesheet/GID1A_test.csv'
+    fasta = params.pipelines_testdata_base_path + 'deepmutscan/testdata/GID1A.fasta'
+    reading_frame = 352-1383
+    min_counts = 2
+    mutagenesis_type = max_diff_to_wt
+    run_seqdepth = true
+    fitness = true
 }
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -50,7 +50,7 @@
                     "type": "integer",
                     "description": "minimum counts for variant to be recognized. All variants below min_counts will be set to 0",
                     "minimum": 1,
-                    "default": 3
+                    "default": 10
                 },
                 "sliding_window_size": {
                     "type": "integer",
@@ -262,7 +262,7 @@
                     "type": "string",
                     "fa_icon": "far fa-check-circle",
                     "description": "Base URL or local path to location of pipeline test dataset files",
-                    "default": "https://raw.githubusercontent.com/BenjaminWehnert1008/test-datasets/dmsqc/dmsqc/",
+                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
                     "hidden": true
                 },
                 "trace_report_suffix": {

diff --git a/testdata/README.md b/testdata/README.md
diff --git a/testdata/input1_50k_1.fastq.gz b/testdata/input1_50k_1.fastq.gz
diff --git a/testdata/input1_50k_2.fastq.gz b/testdata/input1_50k_2.fastq.gz
diff --git a/testdata/input2_50k_1.fastq.gz b/testdata/input2_50k_1.fastq.gz
diff --git a/testdata/input2_50k_2.fastq.gz b/testdata/input2_50k_2.fastq.gz
diff --git a/testdata/output1_50k_1.fastq.gz b/testdata/output1_50k_1.fastq.gz
diff --git a/testdata/output1_50k_2.fastq.gz b/testdata/output1_50k_2.fastq.gz
diff --git a/testdata/output2_50k_1.fastq.gz b/testdata/output2_50k_1.fastq.gz
diff --git a/testdata/output2_50k_2.fastq.gz b/testdata/output2_50k_2.fastq.gz