diff --git a/Rmd/Sample_QC.Rmd b/Rmd/Sample_QC.Rmd
index cfe0ecc5..a7c8efdc 100644
--- a/Rmd/Sample_QC.Rmd
+++ b/Rmd/Sample_QC.Rmd
@@ -1093,6 +1093,7 @@ if (!is.na(batch_var)) {
 QAQC_metadata_subset <- QAQC_annotated %>%
   dplyr::select(unlist(exp_groups), !!ensym(batch_var),
                 NMR_data, FMR_data, Ncov5_data, Nsig80_data, Gini_data)
+  QAQC_metadata_subset[,batch_var] <- factor(QAQC_metadata_subset[,batch_var])
 } else {
     QAQC_metadata_subset <- QAQC_annotated %>%
     dplyr::select(unlist(exp_groups),
@@ -1100,14 +1101,14 @@ QAQC_metadata_subset <- QAQC_annotated %>%
 }
 
 QAQC_metadata_subset %>%
-    summarise_each(levels(as.factor(.))) %>% tally()
+    summarise_all(~length(unique(.))) # Just info. Output not used
+    #summarise_each(levels(as.factor(.))) %>% tally()
 
 potential_covariates <- QAQC_metadata_subset %>%
   dplyr::mutate_all(as.factor) %>%
   purrr::map(levels) %>%
   purrr::map(length)
 
-QAQC_metadata_subset[,batch_var] <- factor(QAQC_metadata_subset[,batch_var])
 
 covariate_names <- names(potential_covariates[potential_covariates < 24])
 
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 3cb872e1..b95ed495 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -417,6 +417,7 @@ if common_config["platform"] =="RNA-Seq":
         params:
             annotations = genome_dir / pipeline_config["annotation_filename"],
             genome_name = pipeline_config["genome_name"],
+            genome_dir = pipeline_config["genomedir"]
         output:
             directory(genome_dir / "RSEM_index"),
         conda:
@@ -424,7 +425,7 @@ if common_config["platform"] =="RNA-Seq":
         benchmark: log_dir / "benchmark.RSEM_make_index.txt"
         shell:
             '''
-            mkdir RSEM_index
+            mkdir {params.genome_dir}/RSEM_index
             rsem-prepare-reference --gtf {params.annotations} {input.genome} {output}/{params.genome_name}
             '''