fixed limma

Author: LuLeom

src/methods/limma_remove_batch_effect/config.vsh.yaml

@@ -19,13 +19,16 @@ links:
 resources:
   - type: r_script
     path: script.R
+  - type: r_script
+    path: /src/utils/helper_functions.R
 
 engines:
   - type: docker
     image: openproblems/base_r:1
     setup:
       - type: r
         bioc: limma
+        packages: [ lifecycle, vctrs, dplyr, rlang ]
 
 runners:
   - type: executable

src/methods/limma_remove_batch_effect/script.R

@@ -11,8 +11,11 @@ meta <- list(
 )
 ## VIASH END
 
+source(paste0(meta$resources_dir, "/helper_functions.R"))
+
 cat("Reading input files\n")
-input <- anndata::read_h5ad(par[["input"]])
+input <- anndata::read_h5ad(par[["input"]]) |>
+  subset_nocontrols()
 
 cat("Subset data\n")
 data_not_correct <- input[, !input$var$to_correct]