Fix tximport summarizedexperiment (#6638)

* SummarizedExperiment: don't sanitise column names * tximport: explicitly disable name sanitisation
nf-core · Sep 13, 2024 · 625fbbc · 625fbbc
1 parent ad30f90
commit 625fbbc
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diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/templates/summarizedexperiment.r b/modules/nf-core/summarizedexperiment/summarizedexperiment/templates/summarizedexperiment.r
@@ -13,7 +13,7 @@ library(SummarizedExperiment)
 #'
 #' @return output Data frame
 
-read_delim_flexible <- function(file, header = TRUE, row.names = NULL, check.names = TRUE, stringsAsFactors = FALSE){
+read_delim_flexible <- function(file, header = TRUE, row.names = NULL, check.names = FALSE, stringsAsFactors = FALSE){
 
     ext <- tolower(tail(strsplit(basename(file), split = "\\\\.")[[1]], 1))
 

diff --git a/modules/nf-core/tximeta/tximport/templates/tximport.r b/modules/nf-core/tximeta/tximport/templates/tximport.r
@@ -26,7 +26,7 @@ library(tximport)
 #' @return A data frame combining the first two columns of the rowData with the assay data from the specified slot.
 
 build_table <- function(se.obj, slot) {
-    cbind(rowData(se.obj)[,1:2], assays(se.obj)[[slot]])
+    data.frame(cbind(rowData(se.obj)[,1:2], assays(se.obj)[[slot]]), check.names = FALSE)
 }
 
 #' Write a table to a file from a SummarizedExperiment object with given parameters