diff --git a/inst/scripts/pqtl-genome-scan.R b/inst/scripts/pqtl-genome-scan.R
index 4e2b6539974ebb9614dac1c408a3e052f01a7822..0b297add8e816494ff7af3a6fefec8cdd28ccb04 100644
--- a/inst/scripts/pqtl-genome-scan.R
+++ b/inst/scripts/pqtl-genome-scan.R
@@ -8,11 +8,9 @@ library(qtl2)
 args <- commandArgs(trailingOnly = TRUE)
 
 #prev args
-qtldata <- args[1] #path to yaml file required to create crossdata object (is that still needed ?)
-crossdata_path <- args[2] #path to crossdata object
-clean_pr_path <- args[3]  #path to genoprobs objects
-kloco_path <- args[4]  #path to kinship (loco) objects
-cores <- args[5] #nb of cores 
+crossdata_path <- args[1] #path to crossdata object
+clean_pr_path <- args[2]  #path to genoprobs objects
+kloco_path <- args[3]  #path to kinship (loco) objects
 
 #as of now (not using args)
 # qtldata <- "TEST.yaml"
@@ -22,11 +20,14 @@ cores <- args[5] #nb of cores
 # cores <- 1
 
 
-#novel args re: covar
-isSexCovar <- args[6] #sexcovar: drop-down menu perhaps ? two options, either yes or no. if yes, extraction of sexcovar and put in model. if no, nope. 
-whichAddCovars <- args[7] #addcovars: at most 2 non-sex covar
-#rémi, re: addcovars (else see issue). This can be a drop down menu (or two drop-down menus? but whatif only one covar is selected?) listing all possible covars existing in covar file (BUT sex covar). Only two of them at most can be selected, perhaps a 
+# novel args re: covar
+# sexcovar: drop-down menu perhaps ? two options, either yes or no. if yes, extraction of sexcovar and put in model. if no, nope.
+isSexCovar <- args[4]
+whichAddCovars <- args[5] #addcovars: at most 2 non-sex covar
+#rémi, re: addcovars (else see issue). This can be a drop down menu (or two drop-down menus? but whatif only one covar is selected?) listing all possible covars existing in covar file (BUT sex covar). Only two of them at most can be selected, perhaps a
 ##remi: il faudrait pouvoir proposer un champ "none" (pour aucun ajout de covar), dans ce cas whichAddCovars <- NULL
+cores <- args[6] #nb of cores
+
 
 #as of now
 # isSexCovar <- 'yes'
@@ -44,17 +45,21 @@ dir.create("outfiles/Rdata")
 ## ----def covars--------------------------------------------
 
 ##---------extract Xcovar (under the condition that the user spec he wants to apply a sex covar)------
-if (isSexCovar=="yes") {
+if (isSexCovar == "yes") {
   Xcovar <- get_x_covar(crossdata)
-} 
+}
 
 ###-------- as for addcovars: if whichAddCovars is not null (exists at least 1 covar besides sex), generates the covar formula for model matrix and all what follows.
-if (!is.null(whichAddCovars)==TRUE) {
-  covar.formula <- as.formula(sprintf("~ 0 + %s", gsub(",", "+", whichAddCovars))) #mk the covar formula for model matrix (tested, works with 1 & 2 addcovars)
-  covar.modmat <- model.matrix(covar.formula,data = crossdata$covar) #get the model matrix out of it
-  covar.modmat <- covar.modmat[,-1, drop=FALSE] # omit the first column bkos k-1 levels; drop=FALSE ensures it stays as a matrix 
-  rownames(covar.modmat) <- rownames(crossdata$covar) #rownames should have remained identical but still, better safe than sorry
-} 
+if (!is.null(whichAddCovars) == TRUE) {
+  covar.formula <-
+    as.formula(sprintf("~ 0 + %s", gsub(",", "+", whichAddCovars))) #mk the covar formula for model matrix (tested, works with 1 & 2 addcovars)
+  covar.modmat <-
+    model.matrix(covar.formula, data = crossdata$covar) #get the model matrix out of it
+  covar.modmat <-
+    covar.modmat[,-1, drop = FALSE] # omit the first column bkos k-1 levels; drop=FALSE ensures it stays as a matrix
+  rownames(covar.modmat) <-
+    rownames(crossdata$covar) #rownames should have remained identical but still, better safe than sorry
+}
 
 #there could be a simpler way,actually ?: addcovar <- model.matrix(~Study, data = pheno)[,-1] (but I prefer the longer one...)
 
@@ -69,13 +74,45 @@ if (!is.null(whichAddCovars)==TRUE) {
 
 
 if (exists("Xcovar") & exists("covar.modmat")) {
-  out <- scan1(genoprobs = clean_pr, pheno = crossdata$pheno, kinship = kloco, addcovar = covar.modmat, Xcovar = Xcovar, cores = cores, max_batch = 1) ##sex covar AND addcovar
-} else if(exists("Xcovar") & !exists("covar.modmat")) {
-  out <- scan1(genoprobs = clean_pr, pheno = crossdata$pheno, kinship = kloco, Xcovar = Xcovar, cores = cores, max_batch = 1) ##sexcovar but no addcovar
-} else if(!exists("Xcovar") & exists("covar.modmat")) {
-  out <- scan1(genoprobs = clean_pr, pheno = crossdata$pheno, kinship = kloco, addcovar = covar.modmat, cores = cores, max_batch = 1)  ##addcovar but no sexcovar
+  out <-
+    scan1(
+      genoprobs = clean_pr,
+      pheno = crossdata$pheno,
+      kinship = kloco,
+      addcovar = covar.modmat,
+      Xcovar = Xcovar,
+      cores = cores,
+      max_batch = 1
+    ) ##sex covar AND addcovar
+} else if (exists("Xcovar") & !exists("covar.modmat")) {
+  out <-
+    scan1(
+      genoprobs = clean_pr,
+      pheno = crossdata$pheno,
+      kinship = kloco,
+      Xcovar = Xcovar,
+      cores = cores,
+      max_batch = 1
+    ) ##sexcovar but no addcovar
+} else if (!exists("Xcovar") & exists("covar.modmat")) {
+  out <-
+    scan1(
+      genoprobs = clean_pr,
+      pheno = crossdata$pheno,
+      kinship = kloco,
+      addcovar = covar.modmat,
+      cores = cores,
+      max_batch = 1
+    )  ##addcovar but no sexcovar
 } else {
-  out <- scan1(genoprobs = clean_pr, pheno = crossdata$pheno, kinship = kloco, cores = cores, max_batch = 1) ##neither addcovar nor sexcovar
+  out <-
+    scan1(
+      genoprobs = clean_pr,
+      pheno = crossdata$pheno,
+      kinship = kloco,
+      cores = cores,
+      max_batch = 1
+    ) ##neither addcovar nor sexcovar
 }
 
 
@@ -103,17 +140,17 @@ test_datplot <- data.frame(
   pos = unlist(crossdata$pmap),
   lod = out
 )
-# !!! Remi !! the lod csv file now contains SEVERAL phenotypes - perhaps drop down menu to viz them ?? 
+# !!! Remi !! the lod csv file now contains SEVERAL phenotypes - perhaps drop down menu to viz them ??
 
 write.csv(test_datplot, "outfiles/LOD/lod.csv", row.names = FALSE)
 save(out, file = "outfiles/Rdata/out.dat")
 #if exists, save the covariate files
 if (exists("covar.modmat")) {
-  save(covar.modmat,file="outfiles/Rdata/covar.modmat.dat")
+  save(covar.modmat, file = "outfiles/Rdata/covar.modmat.dat")
 }
 if (exists("Xcovar")) {
-  save(Xcovar,file="outfiles/Rdata/Xcovar.dat")
-} 
-#save(pr, file = "outfiles/Rdata/pr.dat") #not needed, already existing 
-#save(crossdata, file = "outfiles/Rdata/crossdata.dat") #not needed, already existing 
-#save(kinship, file = "outfiles/Rdata/kinship.dat") #not needed, already existing 
+  save(Xcovar, file = "outfiles/Rdata/Xcovar.dat")
+}
+#save(pr, file = "outfiles/Rdata/pr.dat") #not needed, already existing
+#save(crossdata, file = "outfiles/Rdata/crossdata.dat") #not needed, already existing
+#save(kinship, file = "outfiles/Rdata/kinship.dat") #not needed, already existing