diff --git a/src/depiction_targeted_preproc/pipeline_config/artifacts_mapping.py b/src/depiction_targeted_preproc/pipeline_config/artifacts_mapping.py index f76b528..2aae08c 100644 --- a/src/depiction_targeted_preproc/pipeline_config/artifacts_mapping.py +++ b/src/depiction_targeted_preproc/pipeline_config/artifacts_mapping.py @@ -19,14 +19,14 @@ ], PipelineArtifact.DEBUG: [ "qc/plot_marker_presence_cv.pdf", - "qc/plot_spectra_for_marker.pdf", + #"qc/plot_spectra_for_marker.pdf", # "qc/plot_sample_spectra_before_after.pdf", "qc/plot_peak_counts.pdf", "cluster_default_kmeans.hdf5", "cluster_default_stats_kmeans.csv", "cluster_default_kmeans.png", "cluster_default_hdbscan.png", - "qc/plot_marker_presence_mini.pdf", + #"qc/plot_marker_presence_mini.pdf", ], } diff --git a/src/depiction_targeted_preproc/pipeline_config/default.yml b/src/depiction_targeted_preproc/pipeline_config/default.yml index df0755e..5f15c03 100644 --- a/src/depiction_targeted_preproc/pipeline_config/default.yml +++ b/src/depiction_targeted_preproc/pipeline_config/default.yml @@ -3,10 +3,13 @@ baseline_adjustment: window_size: 3000 window_unit: ppm peak_picker: - peak_picker_type: BasicInterpolated - min_prominence: 0.5 - min_distance: 0.9 - min_distance_unit: mz + peak_picker_type: MSPeakPicker + fit_type: quadratic +#peak_picker: +# peak_picker_type: BasicInterpolated +# min_prominence: 0.5 +# min_distance: 0.9 +# min_distance_unit: mz calibration: calibration_method: RegressShift max_distance: 3000