Get the pipeline intraface(s)

Extracts the pipeline interface(s) as a list of Config-class objects

getPipelineInterfaces(.Object)

# S4 method for Project
getPipelineInterfaces(.Object)

Arguments

.Object	an object of Project-class

Value

a list of objects of Config-class (list-like representation of the YAML file(s)). Number of elements in the list reflects the number of pipeline interfaces defined by the Project-class object.

Methods (by class)

• Project: extracts pipeline interfaces defined in a Project-class object

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
getPipelineInterfaces(p)
#> [[1]]
#> Config object. Class: Config
#>  protocol_mapping:
#>     PROTO1: pipeline1.py
#>     PROTO2: pipeline2.py
#>  pipelines:
#>     pipeline1.py:
#>         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:
#>         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
#> 
#> [[2]]
#> Config object. Class: Config
#>  protocol_mapping:
#>     PROTO1: other_pipeline1.py
#>     PROTO2: other_pipeline2.py
#>  pipelines:
#>     other_pipeline1.py:
#>         name: OTHER_PIPELINE1
#>         path: pipelines/other_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: 
#> other_pipeline1/{sample.sample_name}_{sample.Sample_geo_accession}_1.bw
#>             output2: 
#> other_pipeline1/{sample.sample_name}_{sample.Sample_geo_accession}_2.bw
#>         bioconductor:
#>             readFunName: readData
#>             readFunPath: readData.R
#>     other_pipeline2.py:
#>         name: OTHER_PIPELINE2
#>         path: pipelines/other_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: 
#> other_pipeline2/{sample.sample_name}_{sample.Sample_geo_accession}_1.bw
#>             output2: 
#> other_pipeline2/{sample.sample_name}_{sample.Sample_geo_accession}_2.bw
#>         bioconductor:
#>             readFunName: readData
#>             readFunPath: readData.R
#>