Revert "Made update in response to merge from novartis branch"

jjacobson95 · jjacobson95 · commit b958e83a9875 · 2025-07-24T09:34:19.000-07:00
This reverts commit e811969.
diff --git a/build/mpnst/03_get_experiments.R b/build/mpnst/03_get_experiments.R
@@ -239,15 +239,13 @@ fwrite(pdx_data, file.path("/tmp", paste0(out_prefix, "_pdx_curve_data.tsv")), s
 
 message("Wrote PDX curve data")
 
-
 system(sprintf(
-  "/opt/venv/bin/python calc_pdx_metrics.py %s --drugfile %s --outprefix %s --source 'NF Data Portal' --study 'MPNST PDX'",
-  paste0("/tmp/", out_prefix, "_pdx_curve_data.tsv"),
-  drugfile,
-  paste0("/tmp/", out_prefix, "_pdx")
+  "/opt/venv/bin/python calc_pdx_metrics.py %s --drugfile %s --outprefix %s",
+ paste0("/tmp/", out_prefix, "_pdx_curve_data.tsv"),
+ drugfile,
+ paste0("/tmp/", out_prefix, "_pdx")
 ))
 
-
 message("Wrote PDX experiments to ", "/tmp/",  out_prefix, "_pdx_experiments.tsv and combinations")
 
 
