genWorkenvir |
Generates workflow templates provided by systemPipeRdata helper package / or from the individuals’ pipelines packages |
Build |
SPRproject |
Constructs ts SYSargsList workflow control module (S4 object) from script file |
Build |
SYSargsList |
Constructs SYSargsList workflow control module (S4 object) from parameters descriptions |
Build |
LineWise |
Constructs SYSargsList workflow control module (S4 object) from R-based code |
Build |
importWF |
Constructs SYSargsList object from RMarkdown file |
Build |
runWF |
Executes command-line software and R-code specified in SYSargsList instances |
Run |
clusterRun |
Runs command-line software and R-code steps in parallel mode on a computer cluster |
Run |
plotWF |
Plot visual workflow designs and topologies with different graphical layouts |
Visual |
renderLogs |
Render Technical Report based on RMarkdown |
Report |
statusWF |
Return the overview of the workflow steps computational status |
Print |
stepsWF |
Return the overview of the workflow steps |
Print |
targetsWF |
Return the targets files for each workflow steps |
Print |
outfiles |
Return the expected outfiles files for each workflow steps |
Print |
dependency |
Return the dependency tree for all workflow steps |
Print |
projectInfo |
Return the project paths |
Print |
runInfo |
Return the workflow steps execution configurations |
Print |
baseCommand |
Print the base command for all SYSargs2 steps |
Print |
SampleName |
Print the targets ID for SYSargs2 steps |
Print |
stepName |
Print the workflow step name |
Print |
targetsheader |
Print the target files additional information |
Print |
yamlinput |
Print the input values and variables |
Print |
cmdlist |
Print the rendered command-line for all SYSargs2 steps |
Print |
codeLine |
Print the R-code lines for the LineWise steps |
Print |
baseCommand |
Print the base command for the SYSargs2 steps |
Print |
viewEnvir |
View the R object created in the workflow execution |
Print |
copyEnvir |
Copy the R object created in the workflow execution |
Print |
subset |
Subset the workflow |
Print |
getColumn |
Return the targets or outfiles for one workflow step |
Print |
dependency |
Replace the dependency value of the workflow steps computational status |
Config |
appendStep |
Append a new step in SYSargsList workflow |
Config |
replaceStep |
Replace a step in the SYSargsList workflow |
Config |
renameStep |
Rename a step in the SYSargsList workflow |
Config |
yamlinput |
Replace input values in a SYSargs2 step |
Config |
appendCodeLine |
Append a new LineWise step in SYSargsList workflow |
Config |
replaceCodeLine |
Replace a LineWise step in SYSargsList workflow |
Config |
updateColumn |
Replace or append a column in the targets or outfiles |
Config |
createParam |
Create CWL parametres files from command-line |
Config |
sal2bash |
Export a workflow to bash script |
Export |
sal2rmd |
Export a workflow to R Markdown file |
Export |