improved excel example

dge_workflow/dge_master_template.sh

@@ -52,7 +52,6 @@ dge_fastqc $(ls *fastq.gz) &
 mcdir $baseDir/lanereps_pooled
 
 echo '
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.10/R/core_commons.R")
 options(java.parameters = "-Xmx4g" ); library(xlsx)
 
 sheetFile <- "../originals/natalied-FC_SN678_338-2015-5-12.xls"
@@ -64,10 +63,8 @@ sheetFile <- "../originals/natalied-FC_SN678_338-2015-5-12.xls"
 ## first number : biological repliciate
 ## last number: time
 
-#str_replace_all(x, c("[ad]" = "!", "[cf]" = "?"))
-#install.packages("stringr")
-
 renaming_scheme=c("NC" = "no_culture", "NA" = "no_hormone", "ECD"="ecdysone_", "INS"="insulin_", "9"="9h", "4"="4h")
+
 sampleSheet <- read.xlsx2(sheetFile, "Fastqfiles") %>%
     select(File, SampleName) %>%
     mutate(