diff options
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 7 |
1 files changed, 3 insertions, 4 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index 50008cf..c2c8caa 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -49,6 +49,7 @@ input_file_path = file.path(opt$directory, input_file) if (!(file.exists(input_file_path))) { str_glue("The input file {opt$input_file} path does not exists in the directory {opt$directory}") + stop("The input file does not exists the temp directory") } else { str_glue("The input path for the metadata >>>>>>> {input_file_path}") @@ -89,8 +90,7 @@ default_keys = c( for (item in default_keys) { if (!(item %in% names(json_data))){ - cat("Using FALSE as default parameter for ", item) - cat("\n") + cat("Using FALSE as default parameter for ", item, "\n") json_data[item] = FALSE } } @@ -495,8 +495,7 @@ meffects_plots <- c() # TODO add plots for meffects for (chr in chr_names(dataset)){ - cat("Getting the qtl effect for chromosome", chr) - cat("\n") + cat("Getting the qtl effect for chromosome", chr, "\n") if (dataset$crosstype == "4way"){ coeff_results <- get_qtl_effect(chr, aPr, pheno, LOCO="LOCO", covar = sex) file_name = genRandomFileName(prefix = "RQTL_EFFECT_", file_ext = ".png") |