Error when no partition is defined when creating a workflow

AdrienLeGuillou · AdrienLeGuillou · commit 12b28b52e38e · 2025-06-17T09:46:43.000+02:00
diff --git a/R/utils.R b/R/utils.R
@@ -35,6 +35,8 @@ simple_brew <- function(file_in, placeholder_line, replacement_lines,
 #' @noRd
 create_ctrl_script <- function(wf_summary) {
   sbatch_opts <- wf_summary[["default_sbatch_opts"]]
+  if (!"partition" %in% sbatch_opts)
+    stop("A `partition` option must be defined in `default_sbatch_opts``")
   wf_vars <- make_wf_vars(wf_summary)
 
   relevant_opts <- intersect(names(sbatch_opts), c("account", "partition"))
@@ -60,4 +62,3 @@ create_job_script <- function(wf_summary) {
     replacement_lines = make_sbatch_lines(sbatch_opts)
   )
 }
-
diff --git a/inst/templates/workflow/SWF/controller.sh b/inst/templates/workflow/SWF/controller.sh
@@ -38,4 +38,3 @@ then
 else
     echo "All steps are done"
 fi
-

Original file line number	Diff line number	Diff line change
`@@ -35,6 +35,8 @@ simple_brew <- function(file_in, placeholder_line, replacement_lines,`
`35`	`35`	`#' @noRd`
`36`	`36`	`create_ctrl_script <- function(wf_summary) {`
`37`	`37`	`sbatch_opts <- wf_summary[["default_sbatch_opts"]]`
	`38`	`+ if (!"partition" %in% sbatch_opts)`
	`39`	+ stop("A `partition` option must be defined in `default_sbatch_opts``")
`38`	`40`	`wf_vars <- make_wf_vars(wf_summary)`
`39`	`41`
`40`	`42`	`relevant_opts <- intersect(names(sbatch_opts), c("account", "partition"))`
`@@ -60,4 +62,3 @@ create_job_script <- function(wf_summary) {`
`60`	`62`	`replacement_lines = make_sbatch_lines(sbatch_opts)`
`61`	`63`	`)`
`62`	`64`	`}`
`63`		`-`
-Original file line number
+Diff line change
 else
     echo "All steps are done"
 fi
+-