Add methods to benchmark workflow (#50)

* Add methods to benchmark workflow

* Renaming of some methods

Author: LouisK92

…ap_transcript_assignment/config.vsh.yaml …pt_assignment/clustermap/config.vsh.yamlsrc/methods_transcript_assignment/clustermap_transcript_assignment/config.vsh.yaml renamed to src/methods_transcript_assignment/clustermap/config.vsh.yaml src/methods_transcript_assignment/clustermap_transcript_assignment/config.vsh.yaml renamed to src/methods_transcript_assignment/clustermap/config.vsh.yaml

@@ -1,6 +1,6 @@
 __merge__: /src/api/comp_method_transcript_assignment.yaml
 
-name: clustermap_transcript_assignment
+name: clustermap
 label: "Clustermap Transcript Assignment"
 summary: "Assign transcripts to cells based on the ClusterMap method from He et al. 2021"
 description: "Clusters RNA transcripts using density peak clustering."

…ustermap_transcript_assignment/script.py …anscript_assignment/clustermap/script.pysrc/methods_transcript_assignment/clustermap_transcript_assignment/script.py renamed to src/methods_transcript_assignment/clustermap/script.py src/methods_transcript_assignment/clustermap_transcript_assignment/script.py renamed to src/methods_transcript_assignment/clustermap/script.py

@@ -1,6 +1,6 @@
 __merge__: /src/api/comp_method_transcript_assignment.yaml
 
-name: pciseq_transcript_assignment
+name: pciseq
 label: "pciSeq Transcript Assignment"
 summary: "Assign transcripts to cells using the pciSeq method from Qian et. al. (2020)"
 description: "Uses a reference sc-RNAseq dataset to probabalistically assign cell types and transcripts to cells ."

…eq_transcript_assignment/config.vsh.yaml …script_assignment/pciseq/config.vsh.yamlsrc/methods_transcript_assignment/pciSeq_transcript_assignment/config.vsh.yaml renamed to src/methods_transcript_assignment/pciseq/config.vsh.yaml src/methods_transcript_assignment/pciSeq_transcript_assignment/config.vsh.yaml renamed to src/methods_transcript_assignment/pciseq/config.vsh.yaml

@@ -56,13 +56,24 @@ dependencies:
   - name: control_methods/identity
   - name: control_methods/permute_celltype_annotations
   - name: methods_segmentation/custom_segmentation
+  - name: methods_segmentation/cellpose
+  - name: methods_segmentation/binning
+  - name: methods_segmentation/stardist
+  - name: methods_segmentation/watershed
   - name: methods_transcript_assignment/basic_transcript_assignment
+  - name: methods_transcript_assignment/baysor
+  - name: methods_transcript_assignment/clustermap
+  - name: methods_transcript_assignment/pciseq
   - name: methods_count_aggregation/basic_count_aggregation
   - name: methods_qc_filter/basic_qc_filter
   - name: methods_calculate_cell_volume/alpha_shapes
   - name: methods_normalization/normalize_by_volume
+  - name: methods_normalization/spanorm
   - name: methods_cell_type_annotation/ssam
+  - name: methods_cell_type_annotation/tacco
+  - name: methods_cell_type_annotation/moscot
   - name: methods_expression_correction/gene_efficiency_correction
+  - name: methods_expression_correction/resolvi_correction
   - name: metrics/similarity
 
 runners:

…t/pciSeq_transcript_assignment/script.py …s_transcript_assignment/pciseq/script.pysrc/methods_transcript_assignment/pciSeq_transcript_assignment/script.py renamed to src/methods_transcript_assignment/pciseq/script.py src/methods_transcript_assignment/pciSeq_transcript_assignment/script.py renamed to src/methods_transcript_assignment/pciseq/script.py

@@ -71,7 +71,11 @@ workflow run_wf {
   segm_methods = [
     custom_segmentation.run(
       args: [labels_key: "cell_labels"]
-    )
+    ),
+    cellpose,
+    binning,
+    stardist,
+    watershed
   ]
   segm_ch = init_ch
     | runEach(
@@ -101,7 +105,10 @@ workflow run_wf {
         transcripts_key: "transcripts",
         coordinate_system: "global"
       ]
-    )
+    ),
+    baysor,
+    clustermap,
+    pciseq
   ]
   segm_ass_ch = segm_ch
     | runEach(
@@ -280,30 +287,32 @@ workflow run_wf {
    ****************************************/
 
    // TODO: implement this when direct normalization methods are added
-  direct_norm_methods = []
-  direct_norm_ch = Channel.empty()
-  // direct_norm_ch = qc_filter_ch
-  //   | runEach(
-  //     components: direct_norm_methods,
-  //     id: { id, state, comp ->
-  //       id + "/norm_" + comp.name
-  //     },
-  //     fromState: [
-  //       input: "output_count_aggregation"
-  //     ],
-  //     toState: { id, out_dict, state, comp ->
-  //       state + [
-  //         steps: state.steps + [[
-  //           type: "normalization",
-  //           run_id: id,
-  //           component_id: comp.name,
-  //           input_state: state,
-  //           output_dict: out_dict
-  //         ]],
-  //         output_normalization: out_dict.output
-  //       ]
-  //     }
-  //   )
+  direct_norm_methods = [
+    spanorm
+  ]
+  //direct_norm_ch = Channel.empty()
+   direct_norm_ch = qc_filter_ch
+     | runEach(
+       components: direct_norm_methods,
+       id: { id, state, comp ->
+         id + "/norm_" + comp.name
+       },
+       fromState: [
+         input: "output_count_aggregation"
+       ],
+       toState: { id, out_dict, state, comp ->
+         state + [
+           steps: state.steps + [[
+             type: "normalization",
+             run_id: id,
+             component_id: comp.name,
+             input_state: state,
+             output_dict: out_dict
+           ]],
+           output_normalization: out_dict.output
+         ]
+       }
+     )
 
   /****************************************
    *          COMBINE NORMALIZATION        *
@@ -315,7 +324,9 @@ workflow run_wf {
    *         CELL TYPE ANNOTATION         *
    ****************************************/
   cta_methods = [
-    ssam
+    ssam,
+    tacco,
+    moscot
   ]
   cta_ch = normalization_ch
     | runEach(
@@ -344,7 +355,8 @@ workflow run_wf {
    *         EXPRESSION CORRECTION        *
    ****************************************/
   expr_corr_methods = [
-    gene_efficiency_correction
+    gene_efficiency_correction,
+    resolvi_correction
   ]
   expr_corr_ch = cta_ch
     | runEach(