diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/rqtl_wrapper.R | 6 |
1 files changed, 3 insertions, 3 deletions
diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R index b4725d0..fd786cf 100644 --- a/scripts/rqtl_wrapper.R +++ b/scripts/rqtl_wrapper.R @@ -62,7 +62,7 @@ geno_file = opt$geno pheno_file = opt$pheno # Generate randomized filename for cross object -cross_file = file.path(tmp_dir, "gn3", paste(stri_rand_strings(1, 8), ".cross", sep = "")) +cross_file = file.path(opt$outdir, "gn3", paste(stri_rand_strings(1, 8), ".cross", sep = "")) trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", x) } @@ -288,9 +288,9 @@ if (opt$nperm > 0) { } if (!is.null(opt$filename)){ - out_file = file.path(opt$outdir, "output", opt$filename) + out_file = file.path(opt$outdir, "gn3", opt$filename) } else { - out_file = file.path(opt$outdir, "output", paste(pheno_name, "_", stri_rand_strings(1, 8), sep = "")) + out_file = file.path(opt$outdir, "gn3", paste(pheno_name, "_", stri_rand_strings(1, 8), sep = "")) } if (!is.null(opt$addcovar) || !is.null(opt$control)){ |