From 4e95796cac4052bcc3274b46b9dfcc257b99be71 Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Thu, 29 Aug 2024 20:52:58 +0930
Subject: [PATCH] fix transform assay

---
 R/tranform_assay.R                     | 3 +--
 tests/testthat/test_single_functions.R | 3 +--
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/R/tranform_assay.R b/R/tranform_assay.R
index 1c6669b..b18ceb4 100644
--- 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
index b8282fd..85f350a 100644
--- 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(