SYSargsList Constructor

SYSargsList instances are constructed by the SYSargsList function.

SYSargsList(sysargs = NULL, step_name = "default", 
            targets = NULL, wf_file = NULL, input_file = NULL, dir_path = ".", 
            id = "SampleName",
            inputvars = NULL, rm_targets_col = NULL, 
            dir = TRUE, dependency = NA, 
            run_step = "mandatory",
            run_session = "management",
            run_remote_resources = NULL,
            silent = FALSE, 
            projPath = getOption("projPath", getwd()))

Arguments

sysargs: SYSargs2 object. If the object already exists, it can be used to construct the SYSargsList object.
step_name: character with the step index name.
targets: the path to targets file. The targets file can be either a simple tabular or yml file. Also, it is possible to assign NULL to run the pipeline without the 'targets' file. This can be useful for running specific workflows that do not require input files.
wf_file: name and path to CWL parameters file.
input_file: name and path to input parameters file.
dir_path: full path to the directory with the CWL parameters and input files.
id: A column from targets file, which will be used as an id for each one of the samples. It is required to be unique.
inputvars: Each vector element is required to be defined in the input file, and the names of the elements are needed to match the column names defined in the targets file.
rm_targets_col: targets file colunms to be removed.
dir: This option allows creating an exclusive results folder for each step in the workflow. All the outfiles and log files for the particular step will be created in the respective folders. Default is dir=TRUE.
dependency: character. Dependency tree, required when appending this step to the workflow. Character name of a previous step in the workflow. Default is NA.
run_step: character. If the step has "mandatory" or "optional" flag for the execution.
run_session: character. If the step has "management" or "compute" flag for the execution.
run_remote_resources: List for reserving for each cluster job sufficient computing resources including memory (Megabyte), number of nodes (Int), CPU cores, walltime (Minutes), etc. It is necessary two additional files: conffile and template. conffile is the path to configuration file (default location ./.batchtools.conf.R). This file contains in its simplest form just one command, such as this line for the scheduler: cluster.functions <- makeClusterFunctionsSlurm(template="batchtools.slurm.tmpl"). For more detailed information visit this page: https://mllg.github.io/batchtools/index.html template The template files for a specific queueing/scheduling systems can be downloaded from here: https://github.com/mllg/batchtools/tree/master/inst/templates. Slurm, PBS/Torque, and Sun Grid Engine (SGE) templates are provided within the package demo data.
silent: If set to TRUE, all messages returned by the function will be suppressed.
projPath: a character vector of a full project path name. Default is the current path.

Author

Daniela Cassol

Examples

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'
targetspath <- system.file("extdata/cwl/example/targets_example.txt", 
                            package="systemPipeR")

## Constructor and `appendStep<-`
appendStep(sal) <- SYSargsList(step_name = "echo", 
                               targets=targetspath, dir=TRUE,
                               wf_file="example/workflow_example.cwl", 
                               input_file="example/example.yml", 
                               dir_path = system.file("extdata/cwl", 
                               package="systemPipeR"),
                               inputvars = c(Message = "_STRING_",
                               SampleName = "_SAMPLE_"))
                               
appendStep(sal) <- LineWise(code = {
                            hello <- lapply(getColumn(sal, step=1, 'outfiles'), function(x) yaml::read_yaml(x))
                            }, 
                            step_name = "R_read", 
                            dependency = "echo")
                            
sal
#> Instance of 'SYSargsList': 
#>     WF Steps:
#>        1. echo --> Status: Pending 
#>            Total Files: 3 | Existing: 0 | Missing: 3 
#>          1.1. echo
#>              cmdlist: 3 | Pending: 3
#>        2. R_read --> Status: Pending
#>

Arguments

Author

See also

Examples