Adjust inputs and outputs for building the proper workflow graph and …

…add assertions for method specific required inputs

src/api/comp_assignment_method.yaml

@@ -6,9 +6,17 @@ info:
     description: An assignment method assigns transcripts to cells based on the spatial data and the cell segmentation.
 arguments:
   - name: "--input"
+    required: true
+    direction: input
+    __merge__: file_spatialdata.yaml
+  - name: "--segmentation_input"
+    required: false
+    direction: input
     __merge__: file_spatialdata_segmented.yaml
+  - name: "--input_sc"
+    required: false
     direction: input
-    required: true
+    __merge__: file_singlecell.yaml
   - name: "--output"
     __merge__: file_spatialdata_assigned.yaml
     direction: output
@@ -18,3 +26,6 @@ arguments:
 #     dest: resources_test/common/pancreas
 #   - type: python_script
 #     path: /common/component_tests/run_and_check_output.py
+
+
+

src/api/comp_celltype_annotation_method.yaml

@@ -8,7 +8,15 @@ arguments:
   - name: --input
     required: true
     direction: input
-    __merge__: /src/api/file_spatial_norm_counts.yaml
+    __merge__: file_spatial_norm_counts.yaml
+  - name: --input_transcripts
+    __merge__: file_spatialdata_assigned.yaml
+    direction: input
+    required: false
+  - name: --input_sc
+    required: false
+    direction: input
+    __merge__: file_singlecell.yaml
   - name: --celltype_key
     required: false
     direction: input
@@ -17,7 +25,7 @@ arguments:
   - name: --output
     required: true
     direction: output
-    __merge__: /src/api/file_spatial_with_celltypes.yaml
+    __merge__: file_spatial_with_celltypes.yaml
 # test_resources:
 #   - path: /resources_test/common/pancreas
 #     dest: resources_test/common/pancreas

src/api/comp_expr_correction_method.yaml

@@ -9,6 +9,10 @@ arguments:
     required: true
     direction: input
     __merge__: /src/api/file_spatial_with_celltypes.yaml
+  - name: --input_sc
+    required: false
+    direction: input
+    __merge__: /src/api/file_singlecell.yaml
   - name: --output
     required: true
     direction: output

src/api/comp_normalisation_method.yaml

@@ -9,11 +9,16 @@ arguments:
   - name: --input
     required: true
     direction: input
-    __merge__: /src/api/file_spatial_raw_counts.yaml
+    __merge__: file_spatial_raw_counts.yaml
+  - name: --input_volume
+    type: file
+    description: H5ad with an obs column of cell volumes calculated from spatial transcriptomics data.
+    required: false
+    __merge__: file_cell_volumes.yaml
   - name: --output
     required: true
     direction: output
-    __merge__: /src/api/file_spatial_norm_counts.yaml
+    __merge__: file_spatial_norm_counts.yaml
 
 # test_resources:
 #   - path: /resources_test/common/pancreas

src/assignment_methods/basic/config.vsh.yaml

@@ -1,27 +1,17 @@
 name: basic
 namespace: assignment_methods
 
+__merge__: /src/api/comp_assignment_method.yaml
+
 arguments:
-  - name: --input
-    required: true
-    direction: input
-    __merge__: /src/api/file_spatialdata.yaml
   - name: --transcripts_key
     type: string
     description: The key of the transcripts within the points of the spatial data
     required: true
-  - name: --segmentation_input
-    required: true
-    direction: input
-    __merge__: /src/api/file_spatialdata_segmented.yaml
   - name: --coordinate_system
     type: string
     description: The key of the pixel space coordinate system within the spatial data
     required: true
-  - name: --output
-    required: true
-    direction: output
-    __merge__: /src/api/file_spatialdata_assigned.yaml
 
 resources:
   - type: python_script

src/assignment_methods/basic/script.py

@@ -21,6 +21,10 @@
 # if par['coordinate_system'] == None:
 #    par['coordinate_system'] = 'global'
 
+# Optional parameter check: For this specific assignment method the par['segmentation_input'] is required
+assert par['segmentation_input'] is not None, 'Segmentation input is required for this assignment method.'
+
+
 # Read input
 print('Reading input files', flush=True)
 sdata = sd.read_zarr(par['input'])

src/cell_volume_methods/alpha_shapes/config.vsh.yaml

@@ -1,20 +1,14 @@
 name: alpha_shapes
 namespace: cell_volume_methods
 
+__merge__: /src/api/comp_cell_volume_method.yaml
+
 arguments:
-  - name: --input
-    required: true
-    direction: input
-    __merge__: /src/api/file_spatialdata_assigned.yaml
   - name: --alpha
     type: double
     description: Alpha parameter for calculating the alpha shape (0.0 refers to the convex hull)
     required: false
     default: 0.0
-  - name: --output
-    required: true
-    direction: output
-    __merge__: /src/api/file_cell_volumes.yaml
 
 resources:
   - type: python_script

src/celltype_annotation_methods/ssam/config.vsh.yaml

@@ -1,33 +1,14 @@
 name: ssam
 namespace: celltype_annotation_methods
 
+__merge__: /src/api/comp_celltype_annotation_method.yaml
+
 arguments:
-  - name: --input
-    required: true
-    direction: input
-    __merge__: /src/api/file_spatial_norm_counts.yaml
-  - name: --input_transcripts
-    required: true
-    direction: input
-    __merge__: /src/api/file_spatialdata_assigned.yaml
-  - name: --input_sc
-    required: true
-    direction: input
-    __merge__: /src/api/file_singlecell.yaml
   - name: --um_per_pixel # TODO: Should be able to infer this from transcripts
     required: false
     direction: input
     type: double
     default: 0.5
-  - name: --celltype_key
-    required: false
-    direction: input
-    type: string
-    default: cell_type
-  - name: --output
-    required: true
-    direction: output
-    __merge__: /src/api/file_spatial_with_celltypes.yaml
 
 resources:
   - type: python_script

src/celltype_annotation_methods/ssam/script.py

@@ -18,6 +18,9 @@
 }
 ## VIASH END
 
+# Optional parameter check: For this specific annotation method the par['input_transcripts'] and par['input_sc'] are required
+assert par['input_transcripts'] is not None, 'Transcripts input is required for this annotation method.'
+assert par['input_sc'] is not None, 'Single cell input is required for this annotation method.'
 
 # Read input
 print('Reading input files', flush=True)

src/count_aggregation/basic/config.vsh.yaml

@@ -1,15 +1,7 @@
 name: basic
 namespace: count_aggregation
 
-arguments:
-  - name: --input
-    required: true
-    direction: input
-    __merge__: /src/api/file_spatialdata_assigned.yaml
-  - name: --output
-    required: true
-    direction: output
-    __merge__: /src/api/file_spatial_raw_counts.yaml
+__merge__: /src/api/comp_count_aggregation.yaml
 
 resources:
   - type: python_script

src/expr_correction_methods/gene_efficiency_correction/config.vsh.yaml

@@ -1,24 +1,14 @@
 name: gene_efficiency_correction
 namespace: expr_correction_methods
 
+__merge__: /src/api/comp_expr_correction_method.yaml
+
 arguments:
-  - name: --input
-    required: true
-    direction: input
-    __merge__: /src/api/file_spatial_with_celltypes.yaml
-  - name: --input_sc
-    required: true
-    direction: input
-    __merge__: /src/api/file_singlecell.yaml
   - name: --celltype_key
     required: false
     direction: input
     type: string
     default: cell_type
-  - name: --output
-    required: true
-    direction: output
-    __merge__: /src/api/file_spatial_corrected.yaml
 
 resources:
   - type: python_script

src/expr_correction_methods/gene_efficiency_correction/script.py

@@ -15,6 +15,8 @@
 }
 ## VIASH END
 
+# Optional parameter check: For this specific correction method the par['input_sc'] is required
+assert par['input_sc'] is not None, 'Single cell input is required for this expr correction method.'
 
 # Read input
 print('Reading input files', flush=True)

src/normalisation_methods/normalise_by_volume/config.vsh.yaml

@@ -1,20 +1,7 @@
 name: normalise_by_volume
 namespace: normalisation_methods
 
-arguments:
-  - name: --input
-    required: true
-    direction: input
-    __merge__: /src/api/file_spatial_raw_counts.yaml
-  - name: --input_volume
-    type: file
-    description: H5ad with an obs column of cell volumes calculated from spatial transcriptomics data.
-    required: true
-    __merge__: /src/api/file_cell_volumes.yaml
-  - name: --output
-    required: true
-    direction: output
-    __merge__: /src/api/file_spatial_norm_counts.yaml
+__merge__: /src/api/comp_normalisation_method.yaml
 
 resources:
   - type: python_script

src/normalisation_methods/normalise_by_volume/script.py

@@ -14,6 +14,8 @@
 }
 ## VIASH END
 
+# Optional parameter check: For this specific normalisation method the par['input_volume'] is required
+assert par['input_volume'] is not None, 'Volume input is required for this normalisation method.'
 
 # Read input
 print('Reading input files', flush=True)

src/segmentation_methods/custom/config.vsh.yaml

@@ -1,19 +1,13 @@
 name: custom
 namespace: segmentation_methods
 
+__merge__: /src/api/comp_segmentation_method.yaml
+
 arguments:
-  - name: --input
-    required: true
-    direction: input
-    __merge__: /src/api/file_spatialdata.yaml
   - name: --labels_key
     type: string
     description: The key of the segmentation within the labels of the spatial data
     required: true
-  - name: --output
-    required: true
-    direction: output
-    __merge__: /src/api/file_spatialdata_segmented.yaml
 
 resources:
   - type: python_script