diff --git a/snappy_pipeline/workflows/panel_of_normals/__init__.py b/snappy_pipeline/workflows/panel_of_normals/__init__.py index e409e5642..f6d1dc987 100644 --- a/snappy_pipeline/workflows/panel_of_normals/__init__.py +++ b/snappy_pipeline/workflows/panel_of_normals/__init__.py @@ -81,10 +81,9 @@ panel_of_normals: tools: ['mutect2'] # REQUIRED - available: 'mutect2' path_ngs_mapping: ../ngs_mapping # REQUIRED - size: 10 - shuffle_seed: 1234567 # Configuration for mutect2 mutect2: + path_normals_list: null # Optional file listing libraries to include in panel germline_resource: REQUIRED # Java options java_options: ' -Xmx16g ' @@ -162,6 +161,11 @@ class Mutect2StepPart(PanelOfNormalsStepPart): def __init__(self, parent): super().__init__(parent) + if self.config["mutect2"]["path_normals_list"]: + self.normal_libraries = [] + with open(self.config["mutect2"]["path_normals_list"], "rt") as f: + for line in f: + self.normal_libraries.append(line.strip()) def check_config(self): if self.name not in self.config["tools"]: