suppressPackageStartupMessages(require(Seurat))
suppressPackageStartupMessages(require(SeuratDisk))
suppressPackageStartupMessages(require(scater))
args = commandArgs(trailingOnly=TRUE)
input_paths = args[1]
input_format = args[2]
output = args[3]
initial.options <- commandArgs(trailingOnly = FALSE)
file.arg.name <- "--file="
script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)])
source(paste0(dirname(script.name),"/../R/seurat_io.R"))
# currently giving string with commas in methods, separation happens inside, maybe revert this.
seurat_objects <- read_multiple_seurat4_objects(input_path_list = input_paths, format = input_format)
inputs <- unlist(strsplit(input_paths, split = ","))
if( length(inputs) != length(seurat_objects) ) {
message("List of seurat objects doesn't match list of inputs given")
q(status = 1)
}
saveRDS(seurat_objects, file = output)
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