SPRproject.Rd
Function to construct SYSargsList
workflow control environment (S4 object).
This function creates and checks the directory structure. If the expected directories
are not available, it is possible to create those.
The project directory default structure expected is:
SPRproject/
data/
param/
results/
The project working directory names can be modified, but users need to edit the code accordingly.
a character vector of a full project path name. Default is the current path.
a character vector of a data
directory name. Default is data
.
This subdirectory in the project stores all the raw data, reference, and annotation files.
a character vector of a param
directory name. Default is param
.
This subdirectory in the project stores all the parameter and configuration files.
a character vector of a results
directory name. Default is results
.
This subdirectory in the project stores all the analysis results, including but
not limited: alignment, variant, and peak files (BAM, VCF, BED); tabular result files;
and image/plot files.
a character vector of a logs
directory name. Default is .SPRproject
.
a character vector of SYSargsList
file name which will store all the
project configuration information.
Default is SYSargsList.yml
and it will be save in the logs.dir
folder.
the environment in which workflow will be evaluated. Default will create
a new.env()
.
if set to TRUE
, existing SYSargsList
object saved in the
logs.dir
directory will be used to restart the workflow. This option
will delete all the log files.
if set to TRUE
, existing SYSargsList
object saved in the
logs.dir
directory will be used to resume the workflow.
This argument allows to load the environment and recover all the objects saved
during the workflow execution (please check runWF
function for more
details). This argument can be set as TRUE
when restart = TRUE
or resume = TRUE
are used.
if set to TRUE
, existing logs.dir
directory and all the content,
as logs files and SYSargsList
file will be removed, and a new and
empty SYSargsList
object will be created.
This option should be used with caution!
if set to TRUE, all messages returned by the function will be suppressed.
If an SYSargsList
instance was created before or independent of the
project initialization, it is possible to append this instance after the
project is created. Please see check appendStep<-
function.
SPRproject
will return a SYSargsList
object.
See also as SYSargsList-class
.
sal <- SPRproject(projPath = tempdir())
#> Creating directory: /tmp/Rtmp7ygQ4c/data
#> Creating directory: /tmp/Rtmp7ygQ4c/param
#> Creating directory: /tmp/Rtmp7ygQ4c/results
#> Creating directory '/tmp/Rtmp7ygQ4c/.SPRproject'
#> Creating file '/tmp/Rtmp7ygQ4c/.SPRproject/SYSargsList.yml'
#> Your current working directory is different from the directory chosen for the Project Workflow.
#> For accurate location of the files and running the Workflow, please set the working directory to
#> 'setwd('/tmp/Rtmp7ygQ4c')'
sal
#> Instance of 'SYSargsList':
#> No workflow steps added