some default config changes

fgcz · Jun 18, 2024 · 766a158 · 766a158
1 parent f2ce95c
commit 766a158
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Showing 2 changed files with 9 additions and 6 deletions.
diff --git 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
@@ -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