paramgroups.json

[
    {
        "name": "Inputs (Pick from one group and choose inputs)",
        "description": "Pick from one group, open the group and choose inputs (running with BAM is preferred)",
        "hidden": false
    },
    {
        "name": "Inputs (Pick from one group and choose inputs)/OPTION 1: BAM INPUT",
        "description": "If you have a BAM file of the sample, input it here",
        "hidden": true,
        "parameters": [
            "bam.file"
        ]
    },
    {
        "name": "Inputs (Pick from one group and choose inputs)/OPTION 2: FASTQ INPUT",
        "description": "If you have FASTQ files of the sample, input it here",
        "hidden": true,
        "parameters": [
            "fastq.r1",
            "fastq.r2"
        ]
    },
    {
        "name": "Inputs (Pick from one group and choose inputs)/OPTION 3: Amplicon Classifier (Re-classify Amplicons)",
        "description": "If you have a completed Amplicon Architect sample, you can upload your AA outputs zip file to re-classify using the latest version of Amplicon Classifier. Upload the zip file here.",
        "hidden": true,
        "parameters": [
            "AA_zipped_output"
        ]
    },
    {
        "name": "Required Parameters",
        "description": "",
        "hidden": false,
        "parameters": [
            "Output.File.Prefix",
            "RUN.AA",
            "RUN.AC",
            "minimal.outputs",
            "reference"
        ]
    },
    {
        "name": "Advanced Parameters",
        "description": "",
        "hidden": true,
        "parameters": [
            "cnvkit.segmentation",
            "cnv.bed",
            "AA.seed",
            "normal_bam",
            "VCF.file",
            "VCF.no.filter",
            "CN.gain",
            "Minimum.copy.number.size",
            "Downsample.Argument",
            "AA.runmode",
            "AA.extend.mode",
            "AA.std.of.insert.size",
            "no.filter",
            "skip.QC",
            "ploidy",
            "purity"
        ]
    },
    {
        "name": "Metadata Configuration",
        "description": "If you have extra metadata information.",
        "hidden": true,
        "parameters": [
            "sample_metadata",
            "sample_type",
            "sample_source",
            "tissue_of_origin",
            "reference_genome",
            "run_metadata_file",
            "number_of_AA_amplicons",
            "number_of_AA_features",
            "sample_description"
        ]
    },
    {
        "name": "Job Options: Set to higher limit if running data that is >10x coverage."
    }
]