Fix test for ssam cell type annotation

openproblems-bio · Sep 22, 2024 · ee02a9c · ee02a9c
1 parent 1f9841c
commit ee02a9c
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Showing 3 changed files with 14 additions and 4 deletions.
diff --git a/src/api/comp_method_cell_type_annotation.yaml b/src/api/comp_method_cell_type_annotation.yaml
@@ -1,3 +1,4 @@
+namespace: methods
 info:
   type: method
   subtype: method_cell_type_annotation

diff --git a/src/api/file_spatial_with_cell_types.yaml b/src/api/file_spatial_with_cell_types.yaml
@@ -16,10 +16,6 @@ info:
         name: normalized
         description: Normalized counts
         required: true
-      - type: integer
-        name: lognorm
-        description: Log normalized counts
-        required: true
     obs:
       - type: string
         name: cell_id

diff --git a/src/methods_cell_type_annotation/ssam/config.vsh.yaml b/src/methods_cell_type_annotation/ssam/config.vsh.yaml
@@ -2,6 +2,17 @@ name: ssam
 
 __merge__: /src/api/comp_method_cell_type_annotation.yaml
 
+info:
+  name: ssam
+  type: method
+  label: "SSAM"
+  summary: "Annotate cell types using SSAM"
+  description: "Annotate cell types using SSAM"
+  documentation_url: "https://ssam.readthedocs.io"
+  repository_url: "https://github.com/HiDiHlabs/ssam"
+  references:
+    doi: "10.1038/s41467-021-23807-4"
+
 arguments:
   - name: --um_per_pixel # TODO: Should be able to infer this from transcripts
     required: false
@@ -26,3 +37,5 @@ engines:
 runners:
   - type: executable
   - type: nextflow
+    directives:
+      label: [ midtime, lowcpu, lowmem ]