Change adata loading in spanorm from zellkonverter to anndataR

Author: LouisK92

src/methods_normalization/spanorm/config.vsh.yaml

@@ -18,8 +18,11 @@ engines:
   - type: docker
     image: openproblems/base_r:1
     setup:
+      #- type: docker
+      #  run: |
+      #    apt-get update && apt-get install -y wget
       - type: r
-        bioc: [SpaNorm, zellkonverter]
+        bioc: [SpaNorm, anndataR, rhdf5]
       #- type: r
       #  bioc: [SummarizedExperiment,SingleCellExperiment,SpatialExperiment]
       #  bioc_force_install: true

src/methods_normalization/spanorm/script.R

@@ -1,7 +1,7 @@
 library(SpaNorm)
 library(SingleCellExperiment)
 library(SpatialExperiment)
-library(zellkonverter)
+library(anndataR)
 
 ## VIASH START
 par <- list(
@@ -11,7 +11,7 @@ par <- list(
 ## VIASH END
 
 # Read the input h5ad file and convert to SingleCellExperiment
-sce <- readH5AD(par$input_spatial_aggregated_counts)
+sce <- read_h5ad(par$input_spatial_aggregated_counts, as = "SingleCellExperiment")
 # Convert to SpatialExperiment for SpaNorm
 sce <- as(sce, "SpatialExperiment")
 
@@ -52,4 +52,5 @@ final_sce <- SingleCellExperiment(
 assay(final_sce, "normalized") <- normalized_matrix
 
 # Write the final object to h5ad format
-zellkonverter::writeH5AD(final_sce, par$output)
+dir.create(dirname(par$output), showWarnings = FALSE, recursive = TRUE)
+write_h5ad(final_sce, par$output)