use the new panel processing in the workflow

src/depiction_targeted_preproc/workflow/rules/rules_prepare_pipeline.smk

@@ -1,15 +1,3 @@
-rule prepare_pipeline_standardize_panel:
-    input:
-        csv="{sample}/mass_list.unstandardized.raw.csv",
-    output:
-        csv="{sample}/mass_list.raw.csv",
-    run:
-        from depiction_targeted_preproc.workflow.prepare_pipeline.standardize_table import copy_standardized_table
-        from pathlib import Path
-
-        copy_standardized_table(input_csv=Path(input.csv), output_csv=Path(output.csv))
-
-
 rule prepare_pipeline_write_pipeline_params:
     input:
         params_yml="{sample}/params.yml",

src/depiction_targeted_preproc/workflow/rules/rules_proc.smk

@@ -1,5 +1,3 @@
-
-
 rule process_spectra_config:
     input:
         config="{sample}/pipeline_params.yml",
@@ -35,7 +33,7 @@ rule proc_calibrate:
     input:
         imzml=multiext("{sample}/processed", ".imzML", ".ibd"),
         config="{sample}/config/proc_calibrate.yml",
-        mass_list="{sample}/mass_list.calibration.csv",
+        mass_list="{sample}/panels/calibration.csv",
     output:
         imzml=multiext("{sample}/calibrated", ".imzML", ".ibd"),
         calib_data="{sample}/calib_data.hdf5",
@@ -84,24 +82,3 @@ rule proc_cluster_stats:
     shell:
         "python -m depiction_targeted_preproc.workflow.proc.cluster_stats"
         " --input-netcdf-path {input.netcdf} --output-csv-path {output.csv}"
-
-
-rule proc_mass_list_preparation:
-    input:
-        csv="{sample}/mass_list.raw.csv",
-    output:
-        calibration_csv="{sample}/mass_list.calibration.csv",
-        # TODO remove
-        standards_csv="{sample}/mass_list.standards.csv",
-        # TODO remove
-        visualization_csv="{sample}/mass_list.visualization.csv",
-        # TODO remove
-        visualization_mini_csv="{sample}/mass_list.visualization_mini.csv",
-    shell:
-        """
-        python -m depiction_targeted_preproc.workflow.proc.mass_list_preparation \
-        --raw-csv {input.csv} --out-csv {output.calibration_csv}
-        cp {output.calibration_csv} {output.standards_csv}
-        cp {output.calibration_csv} {output.visualization_csv}
-        cp {output.calibration_csv} {output.visualization_mini_csv}
-        """

src/depiction_targeted_preproc/workflow/rules/rules_qc.smk

@@ -1,7 +1,7 @@
 rule qc_table_marker_surroundings_baseline:
     input:
         imzml=multiext("{sample}/processed", ".imzML", ".ibd"),
-        mass_list="{sample}/mass_list.visualization.csv",
+        mass_list="{sample}/panels/full.csv",
         config="{sample}/pipeline_params.yml",
     output:
         table="{sample}/qc/table_marker_surroundings_baseline.parquet",
@@ -14,7 +14,7 @@ rule qc_table_marker_surroundings_baseline:
 rule qc_table_marker_surroundings_calib:
     input:
         imzml_peaks="{sample}/calibrated.imzML",
-        mass_list="{sample}/mass_list.visualization.csv",
+        mass_list="{sample}/panels/full.csv",
         config="{sample}/pipeline_params.yml",
     output:
         table="{sample}/qc/table_marker_surroundings_calib.parquet",
@@ -81,7 +81,7 @@ rule qc_plot_peak_density_grouped:
 rule qc_plot_calibration_map:
     input:
         calib_data="{sample}/calib_data.hdf5",
-        mass_list="{sample}/mass_list.visualization.csv",
+        mass_list="{sample}/panels/full.csv",
     output:
         pdf="{sample}/qc/plot_calibration_map.pdf",
     shell:
@@ -115,7 +115,7 @@ rule qc_plot_sample_spectra_before_after:
     input:
         imzml_baseline="{sample}/peaks.imzML",
         imzml_calib="{sample}/calibrated.imzML",
-        mass_list="{sample}/mass_list.visualization.csv",
+        mass_list="{sample}/panels/full.csv",
     output:
         pdf="{sample}/qc/plot_sample_spectra_before_after.pdf",
     shell:

src/depiction_targeted_preproc/workflow/rules/rules_simulate.smk

@@ -1,6 +1,7 @@
 # TODO this should be handled differently, i.e. the simulation code should essentially create a new
 #      virtual "sample" maybe not in the raw directory just to be clear about the intentions
 #   -> but then it will require some adjustment in the code that calls it
+# TODO in addition to this above, this might cause conflicts with some of the panel processing rules maybe
 
 
 rule simulate_create_labels:
@@ -19,7 +20,7 @@ rule simulate_create_mass_list:
     input:
         config="{sample}_sim/config/simulate.yml",
     output:
-        mass_list="{sample}_sim/mass_list.raw.csv",
+        mass_list="{sample}_sim/unstandardize_full.csv",
     shell:
         "python -m depiction_targeted_preproc.workflow.simulate.create_mass_list"
         " --config-path {input.config}"
@@ -29,7 +30,7 @@ rule simulate_create_mass_list:
 rule simulate_generate_imzml:
     input:
         image="{sample}_sim/true_labels.hdf5",
-        mass_list="{sample}_sim/mass_list.raw.csv",
+        mass_list="{sample}_sim/full.csv",
         config="{sample}_sim/config/simulate.yml",
     output:
         imzml=multiext("{sample}_sim/raw", ".imzML", ".ibd"),

src/depiction_targeted_preproc/workflow/rules/rules_vis.smk

@@ -2,7 +2,7 @@ rule vis_images:
     input:
         imzml=multiext("{sample}/calibrated", ".imzML", ".ibd"),
         config="{sample}/pipeline_params.yml",
-        mass_list="{sample}/mass_list.visualization.csv",
+        mass_list="{sample}/panels/full.csv",
     output:
         hdf5="{sample}/images_default.hdf5",
     # TODO how can i pass n-jobs nicely here
@@ -60,7 +60,7 @@ rule vis_test_mass_shifts:
     input:
         calib_hdf5="{sample}/calib_data.hdf5",
         config="{sample}/config/proc_calibrate.yml",
-        mass_list="{sample}/mass_list.calibration.csv",
+        mass_list="{sample}/panels/full.csv",
     output:
         hdf5="{sample}/test_mass_shifts.hdf5",
     shell: