Populates and returns output files for a given pipeline

Returns the pipeline outputs which are defined in the pipeline interface indicated in the Project-class

outputsByPipeline(project, ...)

# S4 method for Project
outputsByPipeline(project, pipelineName = NULL)

Arguments

project	Project-class object
...	other arguments passed to methods
pipelineName	pipeline name to return the outputs for

Value

a named list of output file paths for the requested pipeline

Details

Only the samples that have a matching protocol attribute will be used to populate the output paths.

Methods (by class)

• Project: extracts pipeline outputs for a given pipeline

Note

If there are multiple pipeline interfaces that defined the same pipeline (name), the output files of first one will be returned.

If no pipeline name provided, output for all pipelines with unique names are returned

Examples

projectConfig = system.file("extdata",
"example_peps-master",
"example_piface",
"project_config.yaml",
package = "BiocProject")
p = Project(file = projectConfig)
#> Loaded config file: /Users/mstolarczyk/Uczelnia/UVA/code/BiocProject/inst/extdata/example_peps-master/example_piface/project_config.yaml
outputsByPipeline(p, "pipeline2.py")
#> $output1
#> $output1$sample3
#> [1] "/Users/mstolarczyk/Uczelnia/UVA/code/BiocProject/inst/extdata/example_peps-master/example_piface/../output/results_pipeline/sample3//pipeline2/sample3_GSM2471249_1.bw"
#> 
#> 
#> $output2
#> $output2$sample3
#> [1] "/Users/mstolarczyk/Uczelnia/UVA/code/BiocProject/inst/extdata/example_peps-master/example_piface/../output/results_pipeline/sample3//pipeline2/sample3_GSM2471249_2.bw"
#> 
#>