Rename rctd dir and add method to workflow

LouisK92 · LouisK92 · commit 6dc3aa8c0d65 · 2025-12-13T13:14:09.000+01:00
diff --git a/scripts/run_benchmark/run_full_local.sh b/scripts/run_benchmark/run_full_local.sh
@@ -60,6 +60,7 @@ celltype_annotation_methods:
   # - mapmycells
   # - tangram
   # - singler
+  # - rctd
 expression_correction_methods:
   - no_correction
   # - gene_efficiency_correction
diff --git a/scripts/run_benchmark/run_full_seqeracloud.sh b/scripts/run_benchmark/run_full_seqeracloud.sh
@@ -52,6 +52,7 @@ celltype_annotation_methods:
   - mapmycells
   - tangram
   - singler
+  - rctd
 expression_correction_methods:
   - no_correction
   - gene_efficiency_correction
diff --git a/scripts/run_benchmark/run_test_local.sh b/scripts/run_benchmark/run_test_local.sh
@@ -55,6 +55,7 @@ celltype_annotation_methods:
   # - mapmycells
   # - tangram
   # - singler
+  # - rctd
 expression_correction_methods:
   - no_correction
   # - gene_efficiency_correction
diff --git a/scripts/run_benchmark/run_test_seqeracloud.sh b/scripts/run_benchmark/run_test_seqeracloud.sh
@@ -51,6 +51,7 @@ celltype_annotation_methods:
   - mapmycells
   - tangram
   - singler
+  - rctd
 expression_correction_methods:
   - no_correction
   - gene_efficiency_correction
diff --git a/src/methods_cell_type_annotation/rctd/config.vsh.yaml b/src/methods_cell_type_annotation/rctd/config.vsh.yaml
diff --git a/src/methods_cell_type_annotation/rctd/script.R b/src/methods_cell_type_annotation/rctd/script.R
diff --git a/src/workflows/run_benchmark/config.vsh.yaml b/src/workflows/run_benchmark/config.vsh.yaml
@@ -98,7 +98,7 @@ argument_groups:
           A list of cell type annotation methods to run.
         type: string
         multiple: true
-        default: "ssam:tacco:moscot:mapmycells:tangram:singler"
+        default: "ssam:tacco:moscot:mapmycells:tangram:singler:rctd"
       - name: "--expression_correction_methods"
         description: |
           A list of expression correction methods to run.
@@ -171,6 +171,7 @@ dependencies:
   - name: methods_cell_type_annotation/mapmycells
   - name: methods_cell_type_annotation/tangram
   - name: methods_cell_type_annotation/singler
+  - name: methods_cell_type_annotation/rctd
   - name: methods_expression_correction/no_correction
   - name: methods_expression_correction/gene_efficiency_correction
   - name: methods_expression_correction/resolvi_correction
diff --git a/src/workflows/run_benchmark/main.nf b/src/workflows/run_benchmark/main.nf
@@ -377,7 +377,8 @@ workflow run_wf {
     moscot,
     mapmycells,
     tangram,
-    singler
+    singler,
+    rctd
   ]
   
   cta_ch = normalization_ch

Original file line number	Diff line number	Diff line change
`@@ -377,7 +377,8 @@ workflow run_wf {`
`377`	`377`	`moscot,`
`378`	`378`	`mapmycells,`
`379`	`379`	`tangram,`
`380`		`- singler`
	`380`	`+ singler,`
	`381`	`+ rctd`
`381`	`382`	`]`
`382`	`383`
`383`	`384`	`cta_ch = normalization_ch`