Help: TCGA Cancer Drivers Methods

Inputs Outputs References Method




In order to use the workflow you need to:

  • Install Nextflow
  • Clone this repository in a separate directory, and build locally the three Docker images found in it, running the build.sh script within that repo.
  • Run it just using nextflow run main.nf. Arguments specifications:

        Usage:
        Run the pipeline with default parameters:
        nextflow run main.nf
    
        Run with user parameters:
        nextflow run main.nf --predictionsFile {driver.genes.file} --public_ref_dir {validation.reference.file} --participant_name {tool.name} --metrics_ref_dir {gold.standards.dir} --cancer_types {analyzed.cancer.types} --assess_dir {benchmark.data.dir} --results_dir {output.dir}
    
        Mandatory arguments:
                --predictionsFile       List of cancer genes prediction
                --public_ref_dir        Directory with list of cancer genes used to validate the predictions
                --participant_name          Name of the tool used for prediction
                --metrics_ref_dir       Dir that contains metrics reference datasets for all cancer types
                --cancer_types          List of types of cancer selected by the user, separated by spaces
                --assess_dir            Dir where the data for the benchmark are stored
        Other options:
                --results_dir       The output directory where the results will be saved
        Flags:
                --help          Display this message

    Default input parameters and Docker images to use for each step can be specified in the config file