config.json

{
    "command": [
        "Rscript",
        "--vanilla",
        "code/countAmpliconsAWS.R",
        "--rundir",
        "$RUNDIR/",
        "--basespaceID",
        "$BASESPACE_ID",
        "--threads",
        "8",
        "--season",
        "$SEASON"
    ],
    "inputs": {
        "path_args": [
            {
                "env_var_name": "BASESPACE_ID",
                "path_regex": "([^/]+)",
                "path_regex_match_group": 1
            }
        ],
        "query_args": [
            {
                "env_var_name": "SEASON",
                "query_var_name": "season"
            }
        ],
        "body_args": []
    },
    "outputs": {
        "results": {
            "kind": "file",
            "format": "csv",
            "input_path": "LIMS_results.csv",
            "remapped_columns": [
                {
                    "output_name": "plateIndex",
                    "input_name": "Plate_384_Number",
                    "skip_list": ["NA"]
                },
                {
                    "output_name": "plateCell",
                    "input_name": "Sample_Well",
                    "skip_list": ["NA"]
                },
                {
                    "output_name": "marker1",
                    "input_name": "index",
                    "skip_list": ["NA"]
                },
                {
                    "output_name": "marker2",
                    "input_name": "index2",
                    "skip_list": ["NA"]
                },
                {
                    "output_name": "classification",
                    "input_name": "classification"
                }
            ]
        },
        "attachments": [
            "*.pdf",
            "LIMS_results.csv"
        ]
    }
}