fix: fix deseq2 scripts to look for correct column names

boulardlab · Feb 19, 2024 · ffc4537 · ffc4537
1 parent b6f1848
commit ffc4537
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/workflow/scripts/deseq2_starTE_random_v1.R b/workflow/scripts/deseq2_starTE_random_v1.R
@@ -25,7 +25,7 @@ sample_sheet <- read.csv(
     snakemake@input[["sample_sheet"]], 
     sep=",", 
     header=TRUE,
-    row.names = "sample"    
+    row.names = "name"    
 )
 
 print(sample_sheet)

diff --git a/workflow/scripts/deseq2_trna_v1.R b/workflow/scripts/deseq2_trna_v1.R
@@ -25,7 +25,7 @@ sample_sheet <- read.csv(
     snakemake@input[["sample_sheet"]], 
     sep=",", 
     header=TRUE,
-    row.names = "sample"    
+    row.names = "name"    
 )
 
 if ("filename_1" %in% colnames(sample_sheet)) {

diff --git a/workflow/scripts/deseq2_v1.R b/workflow/scripts/deseq2_v1.R
@@ -63,16 +63,16 @@ colData <- fread(sample_sheet)
 
 if ("filename" %in% colnames(colData)) {
   libtype <- "single"
-  if (!all(c("sample", "filename", design_variable) %in% colnames(colData))) {
+  if (!all(c("name", "filename", design_variable) %in% colnames(colData))) {
     stop(
-      sprintf("Wrong columns in sample sheet. Colnames must be: \"sample\", \"filename\" and \"%s\".\nRemove extensions from filename column. Detected column names: %s", design_variable, colnames(colData))
+      sprintf("Wrong columns in sample sheet. Colnames must be: \"name\", \"filename\" and \"%s\".\nRemove extensions from filename column. Detected column names: %s", design_variable, colnames(colData))
     )
   }
 } else if ("filename_1" %in% colnames(colData)) {
   libtype <- "paired"
-  if (!all(c("sample", "filename_1", "filename_2", design_variable) %in% colnames(colData))) {
+  if (!all(c("name", "filename_1", "filename_2", design_variable) %in% colnames(colData))) {
     stop(
-      sprintf("Wrong columns in sample sheet. Colnames must be: \"sample\", \"filename_1\", \"filename_2\", and \"%s\".\nRemove extensions from filename column. Detected column names: %s", design_variable, colnames(colData)))
+      sprintf("Wrong columns in sample sheet. Colnames must be: \"name\", \"filename_1\", \"filename_2\", and \"%s\".\nRemove extensions from filename column. Detected column names: %s", design_variable, colnames(colData)))
   }
 } else {
   stop(sprintf("Could not determine sequencing library type. From the following column names: %s\nPlease, check your column names. They should be all lower case.", colnames(colData)))