Commit cbf5b349 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Accept merge group from args

parent 7c902417
......@@ -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"
......@@ -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"
......@@ -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 "$3"
......@@ -14,6 +14,7 @@ options(future.globals.maxSize= 1000000000000)
option_list=list(
make_option("--p",action="store",default="huPr_PdPb",type='character',help="Project Name"),
make_option("--s",action="store",default="hu",type='character',help="Species")
make_option("--m",action="store",default="Patient",type='character',help="Group to merge on")
)
opt=parse_args(OptionParser(option_list=option_list))
rm(option_list)
......@@ -110,7 +111,7 @@ merges <- NULL
merges <- NULL
for (i in unique(sc10x.groups$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)
}
}
......
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