From cca10ac3e8ccff08f69fb203fae70086c0468667 Mon Sep 17 00:00:00 2001 From: Adrien Le Guillou Date: Wed, 5 Apr 2023 12:11:33 +0200 Subject: [PATCH] fix orphan refs in doc --- R/step_templates.R | 4 ++-- R/workflow.R | 3 +-- man/change_next_workflow_step.Rd | 3 +-- man/step_tmpl_bash_lines.Rd | 4 ++-- man/step_tmpl_bash_script.Rd | 4 ++-- man/step_tmpl_do_call.Rd | 4 ++-- man/step_tmpl_do_call_script.Rd | 4 ++-- man/step_tmpl_map.Rd | 4 ++-- man/step_tmpl_map_script.Rd | 4 ++-- man/step_tmpl_rscript.Rd | 4 ++-- 10 files changed, 18 insertions(+), 20 deletions(-) diff --git a/R/step_templates.R b/R/step_templates.R index 29f2341..ea024dc 100644 --- a/R/step_templates.R +++ b/R/step_templates.R @@ -20,8 +20,8 @@ #' Some basic ones are provided by the `slurmworkflow` package. They instruct #' the workflow to run either a bash script, a set of bash lines given as a #' character vector or an R script. -#' Additional Step Templates can be created to simplify specific tasks, see the -#' `vignette("making-a-custom-step-template")` for details. +#' Additional Step Templates can be created to simplify specific tasks. The +#' easiest way to do so is as wrappers around existing templates. #' #' @export step_tmpl_bash_lines <- function(bash_lines) { diff --git a/R/workflow.R b/R/workflow.R index 157a859..1744f11 100644 --- a/R/workflow.R +++ b/R/workflow.R @@ -138,8 +138,7 @@ get_workflow_root <- function(wf_summary = NULL) { #' Alter the Next Step of a Running Workflow #' #' This function allows a running job to alter the workflow sequence by choosing -#' which step to run after the current one. (See -#' `vignette("altering-the-order-of-steps")`) +#' which step to run after the current one. #' #' @param next_step A scalar number coercible to integer instructing the #' workflow system which step to run next diff --git a/man/change_next_workflow_step.Rd b/man/change_next_workflow_step.Rd index bb67f73..38393f9 100644 --- a/man/change_next_workflow_step.Rd +++ b/man/change_next_workflow_step.Rd @@ -18,8 +18,7 @@ The \code{next_step} value (invisibly) } \description{ This function allows a running job to alter the workflow sequence by choosing -which step to run after the current one. (See -\code{vignette("altering-the-order-of-steps")}) +which step to run after the current one. } \examples{ \dontrun{ diff --git a/man/step_tmpl_bash_lines.Rd b/man/step_tmpl_bash_lines.Rd index c2e95c0..9e93b7f 100644 --- a/man/step_tmpl_bash_lines.Rd +++ b/man/step_tmpl_bash_lines.Rd @@ -21,7 +21,7 @@ Step Templates are helper functions to be used within \code{add_workflow_step}. Some basic ones are provided by the \code{slurmworkflow} package. They instruct the workflow to run either a bash script, a set of bash lines given as a character vector or an R script. -Additional Step Templates can be created to simplify specific tasks, see the -\code{vignette("making-a-custom-step-template")} for details. +Additional Step Templates can be created to simplify specific tasks. The +easiest way to do so is as wrappers around existing templates. } diff --git a/man/step_tmpl_bash_script.Rd b/man/step_tmpl_bash_script.Rd index 04073fe..3ea4dc6 100644 --- a/man/step_tmpl_bash_script.Rd +++ b/man/step_tmpl_bash_script.Rd @@ -21,7 +21,7 @@ Step Templates are helper functions to be used within \code{add_workflow_step}. Some basic ones are provided by the \code{slurmworkflow} package. They instruct the workflow to run either a bash script, a set of bash lines given as a character vector or an R script. -Additional Step Templates can be created to simplify specific tasks, see the -\code{vignette("making-a-custom-step-template")} for details. +Additional Step Templates can be created to simplify specific tasks. The +easiest way to do so is as wrappers around existing templates. } diff --git a/man/step_tmpl_do_call.Rd b/man/step_tmpl_do_call.Rd index eb41983..28a8c2c 100644 --- a/man/step_tmpl_do_call.Rd +++ b/man/step_tmpl_do_call.Rd @@ -30,7 +30,7 @@ Step Templates are helper functions to be used within \code{add_workflow_step}. Some basic ones are provided by the \code{slurmworkflow} package. They instruct the workflow to run either a bash script, a set of bash lines given as a character vector or an R script. -Additional Step Templates can be created to simplify specific tasks, see the -\code{vignette("making-a-custom-step-template")} for details. +Additional Step Templates can be created to simplify specific tasks. The +easiest way to do so is as wrappers around existing templates. } diff --git a/man/step_tmpl_do_call_script.Rd b/man/step_tmpl_do_call_script.Rd index 71b73e0..714d57a 100644 --- a/man/step_tmpl_do_call_script.Rd +++ b/man/step_tmpl_do_call_script.Rd @@ -27,7 +27,7 @@ Step Templates are helper functions to be used within \code{add_workflow_step}. Some basic ones are provided by the \code{slurmworkflow} package. They instruct the workflow to run either a bash script, a set of bash lines given as a character vector or an R script. -Additional Step Templates can be created to simplify specific tasks, see the -\code{vignette("making-a-custom-step-template")} for details. +Additional Step Templates can be created to simplify specific tasks. The +easiest way to do so is as wrappers around existing templates. } diff --git a/man/step_tmpl_map.Rd b/man/step_tmpl_map.Rd index b712c61..b565be6 100644 --- a/man/step_tmpl_map.Rd +++ b/man/step_tmpl_map.Rd @@ -43,7 +43,7 @@ Step Templates are helper functions to be used within \code{add_workflow_step}. Some basic ones are provided by the \code{slurmworkflow} package. They instruct the workflow to run either a bash script, a set of bash lines given as a character vector or an R script. -Additional Step Templates can be created to simplify specific tasks, see the -\code{vignette("making-a-custom-step-template")} for details. +Additional Step Templates can be created to simplify specific tasks. The +easiest way to do so is as wrappers around existing templates. } diff --git a/man/step_tmpl_map_script.Rd b/man/step_tmpl_map_script.Rd index 9e151a8..336118c 100644 --- a/man/step_tmpl_map_script.Rd +++ b/man/step_tmpl_map_script.Rd @@ -30,7 +30,7 @@ Step Templates are helper functions to be used within \code{add_workflow_step}. Some basic ones are provided by the \code{slurmworkflow} package. They instruct the workflow to run either a bash script, a set of bash lines given as a character vector or an R script. -Additional Step Templates can be created to simplify specific tasks, see the -\code{vignette("making-a-custom-step-template")} for details. +Additional Step Templates can be created to simplify specific tasks. The +easiest way to do so is as wrappers around existing templates. } diff --git a/man/step_tmpl_rscript.Rd b/man/step_tmpl_rscript.Rd index faf8e42..db3f6bd 100644 --- a/man/step_tmpl_rscript.Rd +++ b/man/step_tmpl_rscript.Rd @@ -26,7 +26,7 @@ Step Templates are helper functions to be used within \code{add_workflow_step}. Some basic ones are provided by the \code{slurmworkflow} package. They instruct the workflow to run either a bash script, a set of bash lines given as a character vector or an R script. -Additional Step Templates can be created to simplify specific tasks, see the -\code{vignette("making-a-custom-step-template")} for details. +Additional Step Templates can be created to simplify specific tasks. The +easiest way to do so is as wrappers around existing templates. }