scdrake_make | R Documentation |
scdrake
's pipeline plan.This is a wrapper around drake::make()
with some sensible defaults.
Before a plan is executed, this function sets locally some options, environment variables and other things.
That means no side effects are left. Note that this is a less reproducible way to run
the scdrake
pipeline since it is executed in the current R session.
Also note that create_single_sample_dirs()
or create_integration_dirs()
must be run before.
The preferred way is calling the scdrake_r_make()
function,
which is a wrapper around drake::r_make()
(details).
It will start a fresh new R session, source _drake.R
(or a similar file) and execute the plan.
The current _drake.R
-like files copied when a new scdrake
project is initialized are:
_drake_single_sample.R
for the single-sample pipeline
_drake_integration.R
for the integration pipeline
Internally, _drake_single_sample.R
and _drake_integration.R
do almost the same as code in scdrake_make()
,
except there is no need for isolation of side effects. Also, by default, it relies on environment variables,
such as paths to config directories, e.g. SCDRAKE_SINGLE_SAMPLE_CONFIG_DIR
whose value is used as the default for
option used in load_single_sample_configs(dir = getOption("scdrake_single_sample_config_dir"))
.
scdrake_make(
plan,
cfg_pipeline = NULL,
cfg_main = NULL,
verbose = getOption("scdrake_verbose"),
prework = "",
log_worker = TRUE,
options = list(),
...
)
scdrake_r_make(drake_file = NULL, ...)
plan |
A |
cfg_pipeline |
One of:
|
cfg_main |
A |
verbose |
A logical scalar: if |
prework, log_worker, ... |
Passed to |
options |
A list: additional |
drake_file |
A character scalar: path to |
Invisibly TRUE
if plan execution finishes without errors.
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