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LieberInstitute · Oct 23, 2023 · cee249e · cee249e
1 parent 262f044
commit cee249e
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Showing 3 changed files with 12 additions and 12 deletions.
diff --git a/R/array_submit.R b/R/array_submit.R
@@ -50,7 +50,7 @@
 #'
 array_submit <- function(name, task_ids = NULL, submit = FALSE, restore = TRUE, verbose = FALSE) {
     ## Check existence and validity of the shell script
-    if ((basename(name) != name) || !file.exists(paste0(name, '.sh'))) {
+    if ((basename(name) != name) || !file.exists(paste0(name, ".sh"))) {
         stop(
             paste(
                 "'name' must give the name of a shell script in the current",
@@ -59,7 +59,7 @@ array_submit <- function(name, task_ids = NULL, submit = FALSE, restore = TRUE,
         )
     }
 
-    job_original <- readLines(paste0(name, '.sh'))
+    job_original <- readLines(paste0(name, ".sh"))
 
     ############################################################################
     #   Infer failed task IDs if 'task_ids' is NULL
@@ -224,7 +224,7 @@ array_submit <- function(name, task_ids = NULL, submit = FALSE, restore = TRUE,
         paste0("#SBATCH --array=", paste(task_ids, collapse = ","), "%\\1"),
         job_original
     )
-    writeLines(job_new, con = paste0(name, '.sh'))
+    writeLines(job_new, con = paste0(name, ".sh"))
 
     #   Invoke (sbatch) the modified script if requested
     if (submit) {
@@ -233,8 +233,8 @@ array_submit <- function(name, task_ids = NULL, submit = FALSE, restore = TRUE,
     }
 
     # Restore the original script
-    if (restore) writeLines(job_original, con = paste0(name, '.sh'))
+    if (restore) writeLines(job_original, con = paste0(name, ".sh"))
 
     # Return the path
-    return(invisible(paste0(name, '.sh')))
+    return(invisible(paste0(name, ".sh")))
 }
diff --git a/R/job_loop.R b/R/job_loop.R
@@ -25,9 +25,8 @@
 #'     cores = 2
 #' )
 #'
-job_loop <- function(
-        loops, name, create_shell = FALSE, partition = "shared", memory = "10G",
-        cores = 1L, tc = 20, email = "ALL", logdir = "logs") {
+job_loop <- function(loops, name, create_shell = FALSE, partition = "shared", memory = "10G",
+    cores = 1L, tc = 20, email = "ALL", logdir = "logs") {
     ## Check that the loops are correctly defined
     if (!is.list(loops)) {
         stop("'loops' should be a named list.", call. = FALSE)

diff --git a/R/job_single.R b/R/job_single.R
@@ -56,10 +56,11 @@
 #' ## An array job
 #' job_single("jhpce_job_array", task_num = 20, create_logdir = FALSE)
 #'
-job_single <- function(name, create_shell = FALSE, partition = "shared", memory = "10G",
-    cores = 1L, email = "ALL", logdir = "logs", task_num = NULL, tc = 20,
-    command = 'Rscript -e "options(width = 120); sessioninfo::session_info()"',
-    create_logdir = TRUE) {
+job_single <- function(
+        name, create_shell = FALSE, partition = "shared", memory = "10G",
+        cores = 1L, email = "ALL", logdir = "logs", task_num = NULL, tc = 20,
+        command = 'Rscript -e "options(width = 120); sessioninfo::session_info()"',
+        create_logdir = TRUE) {
     ## Remove any spaces
     name <- gsub(" ", "_", name)