From ee02a9c0dfc7c74f7e163c81df0cdb7d29bf25fa Mon Sep 17 00:00:00 2001
From: LouisK92 <37270609+LouisK92@users.noreply.github.com>
Date: Sun, 22 Sep 2024 17:39:54 +0200
Subject: [PATCH] Fix test for ssam cell type annotation

---
 src/api/comp_method_cell_type_annotation.yaml       |  1 +
 src/api/file_spatial_with_cell_types.yaml           |  4 ----
 .../ssam/config.vsh.yaml                            | 13 +++++++++++++
 3 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/src/api/comp_method_cell_type_annotation.yaml b/src/api/comp_method_cell_type_annotation.yaml
index 07d886b1..94ed45a2 100644
--- 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
index bcafed76..8963c845 100644
--- 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
index 209be0e4..f3132496 100644
--- 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 ]
\ No newline at end of file