From 9962398cb81a56dabc497b5d3f4025d1554f6d05 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 8 Jul 2024 21:10:01 +0000 Subject: Pass output directory to R/qtl script instead of pulling it from the environment Also fixes issue where the control marker keyword was wrong --- gn3/api/rqtl.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gn3/api') diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py index 70ebe12..ae0110d 100644 --- a/gn3/api/rqtl.py +++ b/gn3/api/rqtl.py @@ -25,11 +25,11 @@ run the rqtl_wrapper script and return the results as JSON raise FileNotFoundError # Split kwargs by those with values and boolean ones that just convert to True/False - kwargs = ["covarstruct", "model", "method", "nperm", "scale", "control_marker"] + kwargs = ["covarstruct", "model", "method", "nperm", "scale", "control"] boolean_kwargs = ["addcovar", "interval", "pstrata", "pairscan"] all_kwargs = kwargs + boolean_kwargs - rqtl_kwargs = {"geno": genofile, "pheno": phenofile} + rqtl_kwargs = {"geno": genofile, "pheno": phenofile, "outdir": current_app.config.get("TMPDIR")} rqtl_bool_kwargs = [] for kwarg in all_kwargs: if kwarg in request.form: -- cgit v1.2.3