vidarrtest-regression.json.in

[
    {
        "arguments": {
            "ercc.countTotal.jobMemory": null,
            "ercc.countTotal.timeout": null,
            "ercc.countTranscripts.cnv_file": null,
            "ercc.countTranscripts.jobMemory": null,
            "ercc.countTranscripts.modules": null,
            "ercc.countTranscripts.refGenome": null,
            "ercc.countTranscripts.threads": null,
            "ercc.countTranscripts.timeout": null,
            "ercc.fastqR1": {
                "contents": {
                    "configuration": "/.mounts/labs/gsi/testdata/ercc/fastq/SWID_12913657_GCMS_0019_St_P_PE_353_WT_NoGroup_181107_D00343_0247_BCD07KANXX_CAGATC_L007_R1_001.fastq.gz",
                    "externalIds": [
                        {
                            "id": "TEST",
                            "provider": "TEST"
                        }
                    ]
                },
                "type": "EXTERNAL"
            },
            "ercc.fastqR2": {
                "contents": {
                    "configuration": "/.mounts/labs/gsi/testdata/ercc/fastq/SWID_12913657_GCMS_0019_St_P_PE_353_WT_NoGroup_181107_D00343_0247_BCD07KANXX_CAGATC_L007_R2_001.fastq.gz",
                    "externalIds": [
                        {
                            "id": "TEST",
                            "provider": "TEST"
                        }
                    ]
                },
                "type": "EXTERNAL"
            },
            "ercc.makeReport.controlData": null,
            "ercc.makeReport.erccData": null,
            "ercc.makeReport.imagingScriptPath": null,
            "ercc.makeReport.jobMemory": null,
            "ercc.makeReport.modules": null,
            "ercc.makeReport.rScript": null,
            "ercc.mixId": "ERCC Mix 2",
            "ercc.outputFileNamePrefix": "TEST_GCMS_0019",
            "ercc.reference": "hg19",
            "ercc.rpkmTable.erccData": null,
            "ercc.rpkmTable.jobMemory": null,
            "ercc.rpkmTable.modules": null,
            "ercc.rpkmTable.timeout": null,
            "ercc.sampleId": "GCMS_0019"
        },
        "description": "Ercc workflow test",
        "engineArguments": {
           "write_to_cache": false,
           "read_from_cache": false
        },
        "id": "GCMS_0019_DoseRespose",
        "metadata": {
            "ercc.image": {
                "contents": [
                    {
                        "outputDirectory": "@SCRATCH@/@DATE@_Workflow_ercc_GCMS_0019_DoseRespose_@JENKINSID@"
                    }
                ],
                "type": "ALL"
            },
            "ercc.json": {
                "contents": [
                    {
                        "outputDirectory": "@SCRATCH@/@DATE@_Workflow_ercc_GCMS_0019_DoseRespose_@JENKINSID@"
                    }
                ],
                "type": "ALL"
            },
            "ercc.pdf": {
                "contents": [
                    {
                        "outputDirectory": "@SCRATCH@/@DATE@_Workflow_ercc_GCMS_0019_DoseRespose_@JENKINSID@"
                    }
                ],
                "type": "ALL"
            },
            "ercc.rpkmData": {
                "contents": [
                    {
                        "outputDirectory": "@SCRATCH@/@DATE@_Workflow_ercc_GCMS_0019_DoseRespose_@JENKINSID@"
                    }
                ],
                "type": "ALL"
            }
        },
        "validators": [
            {
                "metrics_calculate": "@CHECKOUT@/tests/calculate.sh",
                "metrics_compare": "@CHECKOUT@/tests/compare.sh",
                "output_metrics": "/.mounts/labs/gsi/testdata/ercc/output_metrics/GCMS_0019_DoseRespose.metrics",
                "type": "script"
            }
        ]
    }
]