Merge remote-tracking branch 'origin/master'

dge_workflow/collect_kallisto_data.R

@@ -28,8 +28,8 @@ devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v
 load_pack(knitr)
 load_pack(stringr)
 load_pack(fda)
-library(sleuth)
-library(Rsamtools)
+load_pack(sleuth)
+load_pack(Rsamtools)
 load_pack(tximport)
 
 

dge_workflow/limma/dge_limma.R

@@ -47,7 +47,7 @@ assert(is.null(gene_info_file) || file.exists(gene_info_file), "invalid gene_inf
 designFormula = opts$design
 assert(str_detect(designFormula, "^condition.*")) ## make sure that the condition comes before all batch factors
 
-results_prefix = if (str_length(opts$out) > 0) opts$out else "" # used by add_prefix
+if (!is.null(opts$out)){  results_prefix = opts$out }
 
 pcutoff = if (is.null(opts$pcutoff))NULL else as.numeric(opts$pcutoff)
 qcutoff = if (is.numeric(pcutoff))NULL else as.numeric(opts$qcutoff)