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| author | zsloan | 2024-09-27 18:25:36 +0000 |
|---|---|---|
| committer | zsloan | 2024-09-27 18:25:36 +0000 |
| commit | 4940195460008192b6ca6269e1fb8c172ada4f17 (patch) | |
| tree | 263c606d5ecb7f499232ec3100d112757e9e6582 | |
| parent | 282c3eb8ec6f0e975bedfd8498004112e9087e40 (diff) | |
| download | genenetwork3-4940195460008192b6ca6269e1fb8c172ada4f17.tar.gz | |
Fix R/qtl output paths
The script now takes the --outdir parameter as the output directory, only using TMPDIR if nothing is passed
"output" in the output directory was also changed to "gn3" to be consistent with recent changes to GN3's code
| -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)){ |