pass in file path explicitly

AlexsLemonade · Oct 15, 2024 · 7841c87 · 7841c87
1 parent 8fc6958
commit 7841c87
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/analyses/cell-type-wilms-tumor-06/00_run_workflow.R b/analyses/cell-type-wilms-tumor-06/00_run_workflow.R
@@ -50,7 +50,9 @@ if (!file.exists(homologs_file)) {
     destfile = homologs_file
   )
 }
-system(command = glue::glue("Rscript ", file.path(module_base, "scripts", "prepare-fetal-references.R")))
+system(command = glue::glue(
+  "Rscript {file.path(module_base, 'scripts', 'prepare-fetal-references.R')} --kidney_ref_file {kidney_ref_file}"
+))
 
 # We build the gene position file reference for infercnv ------------------------
 system(command = glue::glue("Rscript ", file.path(module_base, "scripts", "06a_build-geneposition.R")))