Accept merge group from args

bash.scripts/sc10x.RUN.sh

@@ -8,11 +8,11 @@
 #SBATCH --mail-type ALL
 #SBATCH --mail-user gervaise.henry@utsouthwestern.edu
 
-module load python/3.6.4-anaconda 
-source activate umap
+module load python/3.7.x-anaconda 
+conda activate seurat
 module load gdal
 module load cairo/1.14.8
-module load R/3.6.1-gccmkl 
+module load R/4.0.2-gccmkl 
 module load hdf5_18/1.8.17
-Rscript ../r.scripts/sc-TissueMapper_RAW.R --p "$1" --s "$2"
-Rscript ../r.scripts/sc-TissueMapper_ID.R --p "$1" --s "$2" --o "$3"
+Rscript ../r.scripts/sc-TissueMapper_RAW.R --p "$1" --s "$2" --m "$3"
+Rscript ../r.scripts/sc-TissueMapper_ID.R --p "$1" --s "$2" --o "$4"

bash.scripts/sc10x.id.sh

@@ -8,10 +8,10 @@
 #SBATCH --mail-type ALL
 #SBATCH --mail-user gervaise.henry@utsouthwestern.edu
 
-module load python/3.6.4-anaconda 
-source activate umap
+module load python/3.7.x-anaconda 
+conda activate seurat
 module load gdal
 module load cairo/1.14.8
-module load R/3.6.1-gccmkl 
+module load R/4.0.2-gccmkl 
 module load hdf5_18/1.8.17
-Rscript ../r.scripts/sc-TissueMapper_ID.R --p "$1" --s "$2" --o "$3"
+Rscript ../r.scripts/sc-TissueMapper_ID.R --p "$1" --s "$2" --o "$4"

bash.scripts/sc10x.raw.sh

@@ -14,4 +14,4 @@ module load gdal
 module load cairo/1.14.8
 module load R/4.0.2-gccmkl 
 module load hdf5_18/1.8.17
-Rscript ../r.scripts/sc-TissueMapper_RAW.R --p "$1" --s "$2"
+Rscript ../r.scripts/sc-TissueMapper_RAW.R --p "$1" --s "$2" --m "$3"

r.scripts/sc-TissueMapper_RAW.R

@@ -14,6 +14,7 @@ options(future.globals.maxSize= 1000000000000)
 option_list=list(
   make_option("--p",action="store",default="huPr_PdPb",type='character',help="Project Name"),
   make_option("--s",action="store",default="hu",type='character',help="Species")
+  make_option("--m",action="store",default="Patient",type='character',help="Group to merge on")
 )
 opt=parse_args(OptionParser(option_list=option_list))
 rm(option_list)
@@ -110,7 +111,7 @@ merges <- NULL
 merges <- NULL
 for (i in unique(sc10x.groups$Patient[sc10x.groups$Keep==1])){
   for (j in sc10x.groups$Samples[sc10x.groups$Keep==1]){
-    if (sc10x.groups[sc10x.groups$Samples==j,]$Patient==i){
+    if (sc10x.groups[sc10x.groups$Samples==j,][opt$merge]==i){
       merges <- c(merges,j)
     }
   }