Get pipelines by protocol name

Gets the pipelines defined within the pipeline interface

getPipelines(.Object, protocolName = NULL)

# S4 method for Config
getPipelines(.Object, protocolName = NULL)

Arguments

.Object	a pipeline interface, an object of Config-class
protocolName	a string or vector of strings indicating the protocols for which the pipelines should be returned

Value

a list of pipelines, objets of Config-class

Details

To get all the pipelines (default) do not specify any protocolName

Methods (by class)

• Config: extracts pipelines from a pipeline interface

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
pifaces = getPipelineInterfaces(p)
getPipelines(pifaces[[1]])
#> $pipeline1.py
#> Config object. Class: Config
#>  name: PIPELINE1
#>  path: pipelines/pipeline1.py
#>  looper_args: TRUE
#>  required_input_files: read1
#>  all_input_files: read1 read2
#>  ngs_input_files: read1 read2
#>  arguments:
#>     --sample-name: sample_name
#>  outputs:
#>     output1: pipeline1/{sample.sample_name}_{sample.Sample_geo_accession}_1.bw
#>     output2: pipeline1/{sample.sample_name}_{sample.Sample_geo_accession}_2.bw
#>  bioconductor:
#>     readFunName: readData
#>     readFunPath: readData.R
#> 
#> $pipeline2.py
#> Config object. Class: Config
#>  name: PIPELINE2
#>  path: pipelines/pipeline2.py
#>  looper_args: TRUE
#>  required_input_files: read1
#>  all_input_files: read1 read2
#>  ngs_input_files: read1 read2
#>  arguments:
#>     --sample-name: sample_name
#>  outputs:
#>     output1: pipeline2/{sample.sample_name}_{sample.Sample_geo_accession}_1.bw
#>     output2: pipeline2/{sample.sample_name}_{sample.Sample_geo_accession}_2.bw
#>  bioconductor:
#>     readFunName: readData
#>     readFunPath: readData.R
#>