jgi_mg_assembly.spec

/*
A KBase module: jgi_mg_assembly

*/

module jgi_mg_assembly {
    /*
    A boolean - 0 for false, 1 for true.
        @range (0, 1)
    */
    typedef int boolean;
    typedef string assembly_upa;

    /* Should be only Paired-end reads. */
    typedef string reads_upa;

    /*
    Inputs for the Assembly pipeline.
    reads_upa:
        UPA for the input reads object. This should be a Paired-End Illumina reads file.
    workspace_name:
        name of the workspace to upload to at the end.
    output_assembly_name:
        name of the output assembly file.
    skip_rqcfilter:
        If 1, skip the RQCFilter step of the pipeline. If 0, run it. (default = 0)
    cleaned_reads_name (optional):
        If not empty, this will cause the finalized, cleaned/filtered reads to be uploaded as a new
        reads object with this name. This'll be an interleaved paired-end reads object.
    filtered_reads_name (optional, unless alignment_name is present):
        If not empty, this will cause the RQCFiltered reads to be uploaded as a new reads object. These
        are the reads aligned to the final assembly, so these are needed to associate with the
        final alignment if that alignment is to be kept.
    debug (hidden option):
        If 1, run in debug mode. A little more verbose, and trims some parameters from various steps
        so it can run locally(ish). You probably don't want to do this in production, it's meant for
        testing.
    */
    typedef structure {
        reads_upa reads_upa;
        string workspace_name;
        string output_assembly_name;
        string cleaned_reads_name;
        string filtered_reads_name;
        boolean skip_rqcfilter;
        boolean debug;
    } AssemblyPipelineParams;

    /*
    Outputs from the Assembly pipeline.
    report_name:
        The name of the generated report object.
    report_ref:
        The UPA for the generated report object.
    assembly_upa:
        The UPA for the newly made assembly object.
    cleaned_reads_upa (optional):
        The UPA for the finalized, cleaned reads that are assembled in the pipeline, if requested by the input.
    filtered_reads_upa (optional):
        The UPA for the RQCFiltered reads, if requested by the input, AND skip_rqcfilter is not true.
    */
    typedef structure {
        string report_name;
        string report_ref;
        assembly_upa assembly_upa;
        reads_upa cleaned_reads_upa;
        reads_upa filtered_reads_upa;
    } AssemblyPipelineResults;

    funcdef run_mg_assembly_pipeline(AssemblyPipelineParams params)
        returns (AssemblyPipelineResults results) authentication required;
};