vidarrtest-regression.json.in

[
    {
        "arguments": {
            "sequenza.cnvFile": {
                "contents": {
                    "configuration": "/.mounts/labs/gsi/testdata/sequenza/input_data/VARTEST.copynumber",
                    "externalIds": [
                        {
                            "id": "TEST",
                            "provider": "TEST"
                        }
                    ]
                },
                "type": "EXTERNAL"
            },
            "sequenza.formatJson.height": null,
            "sequenza.formatJson.jobMemory": 6,
            "sequenza.formatJson.modules": null,
            "sequenza.formatJson.rScript": null,
            "sequenza.formatJson.sequenzaRmd": null,
            "sequenza.formatJson.summaryPlotScript": null,
            "sequenza.formatJson.width": null,
            "sequenza.gammaRange": null,
            "sequenza.outputFileNamePrefix": "TESTING",
            "sequenza.preprocessInputs.jobMemory": 4,
            "sequenza.preprocessInputs.modules": null,
            "sequenza.preprocessInputs.preprocessScript": null,
            "sequenza.preprocessInputs.rScript": null,
            "sequenza.preprocessInputs.timeout": null,
            "sequenza.runSequenza.cancerType": null,
            "sequenza.runSequenza.female": null,
            "sequenza.runSequenza.genomeSize": null,
            "sequenza.runSequenza.jobMemory": 6,
            "sequenza.runSequenza.minReadsBaf": null,
            "sequenza.runSequenza.minReadsNormal": null,
            "sequenza.runSequenza.modules": null,
            "sequenza.runSequenza.ploidyFile": "$SEQUENZA_RES_ROOT/PANCAN_ASCAT_ploidy_prob.Rdata",
            "sequenza.runSequenza.rScript": null,
            "sequenza.reference": "hg38",
            "sequenza.runSequenza.reference": null,
            "sequenza.runSequenza.sequenzaScript": null,
            "sequenza.runSequenza.timeout": null,
            "sequenza.runSequenza.windowSize": null,
            "sequenza.snpFile": {
                "contents": {
                    "configuration": "/.mounts/labs/gsi/testdata/sequenza/input_data/VARTEST.snp",
                    "externalIds": [
                        {
                            "id": "TEST",
                            "provider": "TEST"
                        }
                    ]
                },
                "type": "EXTERNAL"
            }
        },
        "description": "Sequenza workflow test",
        "engineArguments": {
           "write_to_cache": false,
           "read_from_cache": false
        },
        "id": "VARSCAN_OUTPUTS_PCSI_CHR22",
        "metadata": {
            "sequenza.gammaMarkdownPdf": {
                "contents": [
                    {
                        "outputDirectory": "@SCRATCH@/@DATE@_Workflow_sequenza_VARSCAN_OUTPUTS_PCSI_CHR22_@JENKINSID@"
                    }
                ],
                "type": "ALL"
            },
            "sequenza.gammaSummaryPlot": {
                "contents": [
                    {
                        "outputDirectory": "@SCRATCH@/@DATE@_Workflow_sequenza_VARSCAN_OUTPUTS_PCSI_CHR22_@JENKINSID@"
                    }
                ],
                "type": "ALL"
            },
            "sequenza.resultJson": {
                "contents": [
                    {
                        "outputDirectory": "@SCRATCH@/@DATE@_Workflow_sequenza_VARSCAN_OUTPUTS_PCSI_CHR22_@JENKINSID@"
                    }
                ],
                "type": "ALL"
            },
            "sequenza.resultZip": {
                "contents": [
                    {
                        "outputDirectory": "@SCRATCH@/@DATE@_Workflow_sequenza_VARSCAN_OUTPUTS_PCSI_CHR22_@JENKINSID@"
                    }
                ],
                "type": "ALL"
            }
        },
        "validators": [
            {
                "metrics_calculate": "@CHECKOUT@/tests/calculate.sh",
                "metrics_compare": "@CHECKOUT@/tests/compare.sh",
                "output_metrics": "/.mounts/labs/gsi/testdata/sequenza/output_metrics/VARSCAN_OUTPUTS_PCSI_CHR22.metrics",
                "type": "script"
            }
        ]
    }
]