Import R Markdown file as workflow. Each R code chunk will be set as a step in the
workflow. This operation requires a few extra settings on the R Markdown chunk
options, to include a particular code chunk in the workflow analysis. Please check
importWF( sysargs, file_path, ignore_eval = TRUE, update = FALSE, confirm = FALSE, check_tool = !update, check_module = check_tool, verbose = TRUE )
SYSargsList empty object. More information on
string, file path of the workflow file.
logical, treat all R chunks'
eval option as
TRUE in workflow
Rmd file even if some chunks have
logical, If you have ever changed the template and want to sync new changes,
TRUE to update the workflow. This function will find the
difference between old template and this new template, update line number
records, update preprocessing code, and try to import new steps. The
updated template is useful in
logical, Only useful when you combine
update = TRUE, some questions
will be asked during update. Changing this to
skip these questions and directly say "Yes" to all answers. Useful
in non-interactive mode. Default is to say "No" in non-interactive mode.
logical, whether to check all required tools by this workflow are in PATH (callable).
It uses the
listCmdTools function to perform the check.
The default is the reverse of
update. It means if it is the first importing the workflow, tools and modules
will be checked. If it is updating the existing workflow, tools will not be checked.
logical, whether to check all required modules are available. To do so, a modular system has be to installed.
If no modular system, this check will be skipped, even if
check_module = TRUE.
It uses the
listCmdModules function to perform the check.
Check the help of
module to know more about modular system.
logical, print out verbose message while function running.
importWF will return an
To include a particular code chunk from the R Markdown file in the workflow analysis, please use the following code chunk options:
spr = 'r': for code chunks with R code lines;
spr = 'sysargs': for code chunks with an `SYSargsList` object;
spr.dep = <StepName>: for specify the previous dependency. If this options
is not found, it will automaticly add the previous step.
spr = 'sysargs', the last object assigned needs to be the
spr flag is not found, the R chunk will not be included in the workflow.
It is required to start a project using
SPRproject() function, and use the
object to populate the steps from R Markdown file.
file_path <- system.file("extdata/spr_simple_lw.Rmd", package="systemPipeR") sal <- SPRproject(overwrite = TRUE) #> Recreating directory '/home/runner/work/systemPipeR/systemPipeR/docs/reference/.SPRproject' #> Creating file '/home/runner/work/systemPipeR/systemPipeR/docs/reference/.SPRproject/SYSargsList.yml' sal <- importWF(sal, file_path) #> Reading Rmd file #> #> #> ---- Actions ---- #> Checking chunk eval values #> Checking chunk SPR option #> Ignore non-SPR chunks: 17 #> Parse chunk code #> Checking preprocess code for each step #> No preprocessing code for SPR steps found #> Now importing step 'firstStep' #> Now importing step 'secondStep' #> Now back up current Rmd file as template for `renderReport` #> Template for renderReport is stored at #> /home/runner/work/systemPipeR/systemPipeR/docs/reference/.SPRproject/workflow_template.Rmd #> Edit this file manually is not recommended #> Now check if required tools are installed #> There is no commandline (SYSargs) step in this workflow, skip. #> Import done #>