fix transform assay

MangiolaLaboratory · Aug 29, 2024 · 4e95796 · 4e95796
1 parent 5112300
commit 4e95796
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Showing 2 changed files with 2 additions and 4 deletions.
diff --git a/R/tranform_assay.R b/R/tranform_assay.R
@@ -38,7 +38,7 @@ tranform_assay.HPCell = function(
       user_function = transform_utility |> quote() , 
       input_read_RNA_assay = as.name(target_input), 
       transform_fx = transform |> quote() ,
-      external_path = glue("{input_hpc$initialisation$store}/external")
+      external_path = glue("{input_hpc$initialisation$store}/external") |> as.character()
     )
 
 }
@@ -75,5 +75,4 @@ transform_utility  = function(input_read_RNA_assay, transform_fx, external_path)
       as.sparse=TRUE
     )
 
-  file_name
 }
diff --git a/tests/testthat/test_single_functions.R b/tests/testthat/test_single_functions.R
@@ -548,7 +548,6 @@ file_list =
 
   # Initialise pipeline characteristics
 file_list |> 
-  head(2) |> 
   initialise_hpc(
     gene_nomenclature = "symbol",
     data_container_type = "sce_hdf5",
@@ -578,7 +577,7 @@ file_list |>
   ) |>
 
   # Remove empty outliers
-  remove_empty_DropletUtils( target_input = "data_object") |> 
+  remove_empty_DropletUtils( target_input = "sce_transformed") |> 
 
   # Annotation
   annotate_cell_type(