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vidarrtest-regression.json.in
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[
{
"arguments": {
"starFusion.chimeric": {
"contents": {
"configuration": "/.mounts/labs/gsi/testdata/starfusion/input_data/test.Chimeric.out.junction",
"externalIds": [
{
"id": "TEST",
"provider": "TEST"
}
]
},
"type": "EXTERNAL"
},
"starFusion.inputFqs": [
{
"left": {
"contents": {
"configuration": "/.mounts/labs/gsi/testdata/starfusion/input_data/reads_1.fq.gz",
"externalIds": [
{
"id": "TEST",
"provider": "TEST"
}
]
},
"type": "EXTERNAL"
},
"right": {
"contents": {
"configuration": "/.mounts/labs/gsi/testdata/starfusion/input_data/reads_2.fq.gz",
"externalIds": [
{
"id": "TEST",
"provider": "TEST"
}
]
},
"type": "EXTERNAL"
}
},
{
"left": {
"contents": {
"configuration": "/.mounts/labs/gsi/testdata/starfusion/input_data/reads_1.fq.gz",
"externalIds": [
{
"id": "TEST",
"provider": "TEST"
}
]
},
"type": "EXTERNAL"
},
"right": {
"contents": {
"configuration": "/.mounts/labs/gsi/testdata/starfusion/input_data/reads_2.fq.gz",
"externalIds": [
{
"id": "TEST",
"provider": "TEST"
}
]
},
"type": "EXTERNAL"
}
}
],
"starFusion.reference": "hg38",
"starFusion.outputFileNamePrefix": "STAR-Fusion_golden_data",
"starFusion.runStarFusion.jobMemory": null,
"starFusion.runStarFusion.threads": null,
"starFusion.runStarFusion.timeout": 1
},
"description": "STAR-Fusion workflow test",
"engineArguments": {
"read_from_cache": false,
"write_to_cache": false
},
"id": "STAR-Fusion_golden_data",
"metadata": {
"starFusion.fusionCodingEffects": {
"contents": [
{
"outputDirectory": "@SCRATCH@/@DATE@_Workflow_starFusion_STAR-Fusion_golden_data_@JENKINSID@"
}
],
"type": "ALL"
},
"starFusion.fusions": {
"contents": [
{
"outputDirectory": "@SCRATCH@/@DATE@_Workflow_starFusion_STAR-Fusion_golden_data_@JENKINSID@"
}
],
"type": "ALL"
},
"starFusion.fusionsAbridged": {
"contents": [
{
"outputDirectory": "@SCRATCH@/@DATE@_Workflow_starFusion_STAR-Fusion_golden_data_@JENKINSID@"
}
],
"type": "ALL"
}
},
"validators": [
{
"metrics_calculate": "@CHECKOUT@/tests/calculate.sh",
"metrics_compare": "@CHECKOUT@/tests/compare.sh",
"output_metrics": "/.mounts/labs/gsi/testdata/starfusion/output_metrics/STAR-Fusion_golden_data.metrics",
"type": "script"
}
]
}
]