diff --git a/.examples/Lactobacillus_delbrueckii/project_config.yaml b/.examples/Lactobacillus_delbrueckii/project_config.yaml index d811dda7..a116871b 100644 --- a/.examples/Lactobacillus_delbrueckii/project_config.yaml +++ b/.examples/Lactobacillus_delbrueckii/project_config.yaml @@ -29,4 +29,4 @@ rules: cblaster-genome: TRUE cblaster-bgc: FALSE gecco: TRUE - amrfinderplus: TRUE + amrfinderplus: FALSE diff --git a/workflow/bgcflow/bgcflow/data/gather_amrfinder.py b/workflow/bgcflow/bgcflow/data/gather_amrfinder.py index e296f03d..5befd5e0 100644 --- a/workflow/bgcflow/bgcflow/data/gather_amrfinder.py +++ b/workflow/bgcflow/bgcflow/data/gather_amrfinder.py @@ -53,9 +53,9 @@ def gather_amrfinder(input_list, output_file): dataframes = [] with open(input_list, "r") as f: - data = f.readlines() + data = f.read() - dataframes = pd.concat([cleanup_amrfinder(i.strip("\n")) for i in data]) + dataframes = pd.concat([cleanup_amrfinder(i) for i in data.split()]) dataframes.to_csv(output_file, index=False) return