From 00cd6ee57a8a405e5dbec681bcebdab9b3452260 Mon Sep 17 00:00:00 2001 From: Saori Sakaue Date: Wed, 14 Aug 2024 12:41:55 -0400 Subject: [PATCH] Specified arguments' classes --- Parallelized Bash Script/SCENT_parallelization.R | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/Parallelized Bash Script/SCENT_parallelization.R b/Parallelized Bash Script/SCENT_parallelization.R index c49e57d..f13992d 100644 --- a/Parallelized Bash Script/SCENT_parallelization.R +++ b/Parallelized Bash Script/SCENT_parallelization.R @@ -3,14 +3,13 @@ library(SCENT) ####### INPUTS #Obtain arguments: (from Cluster) -node = as.numeric(commandArgs(trailingOnly = T)[1]) # JOB ARRAY number: node usage -cores = as.numeric(commandArgs(trailingOnly = T)[2]) # numeric. Number of Cores -SCENTobj_rds = commandArgs(trailingOnly = T)[3] # RDS object file type +node = as.integer(commandArgs(trailingOnly = T)[1]) # integer. JOB ARRAY number: node usage +cores = as.integer(commandArgs(trailingOnly = T)[2]) # integer. Number of Cores +SCENTobj_rds = commandArgs(trailingOnly = T)[3] # character. RDS object file type celltype = commandArgs(trailingOnly = T)[4] # character. CellType regr = commandArgs(trailingOnly = T)[5] # character. Regression Type -bin = commandArgs(trailingOnly = T)[6] # logical. Binarize ATAC counts -output_dir = commandArgs(trailingOnly = T)[7] # Output of each text file to a specific folder - +bin = as.logical(commandArgs(trailingOnly = T)[6]) # logical. Binarize ATAC counts +output_dir = commandArgs(trailingOnly = T)[7] # character. Output of each text file to a specific folder ###Example of inputs from the bash script: parallelizedSCENT.sh # node <- 1