vidarrtest-regression.json.in

[
    {
      "arguments": {
          "hlaminer.fastqR1": {
              "contents": {
                  "configuration": "/.mounts/labs/gsi/testdata/hlaminer/input_data/SWID_15949654_CRE_0002_Pb_R_PE_409_WG_200124_A00469_0077_BHNGLTDSXX_GAGACGAT-TAACCGGT_L002_001.annotated.subset_R1.fastq.gz",
                  "externalIds": [
                      {
                          "id": "TEST",
                          "provider": "TEST"
                      }
                  ]
              },
              "type": "EXTERNAL"
          },
          "hlaminer.fastqR2": {
              "contents": {
                  "configuration": "/.mounts/labs/gsi/testdata/hlaminer/input_data/SWID_15949654_CRE_0002_Pb_R_PE_409_WG_200124_A00469_0077_BHNGLTDSXX_GAGACGAT-TAACCGGT_L002_001.annotated.subset_R2.fastq.gz",
                  "externalIds": [
                      {
                          "id": "TEST",
                          "provider": "TEST"
                      }
                  ]
              },
              "type": "EXTERNAL"
          },
          "hlaminer.runHlaMiner.hlaFasta": "$HLAMINER_BWA_INDEX_ROOT/HLA-I_II_GEN.fasta",
          "hlaminer.outputFileNamePrefix": "TESTING",
          "hlaminer.runHlaMiner.pDesignationFile": "$HLAMINER_BWA_INDEX_ROOT/HLAminer_v1.4/database/hla_nom_p.txt",
          "hlaminer.runHlaMiner.hlaMiner": "$HLAMINER_ROOT/bin/HLAminer.pl",
          "hlaminer.runHlaMiner.modules": "hlaminer/1.4 hlaminer-bwa-index/0.7.17 bwa/0.7.17",
          "hlaminer.runHlaMiner.jobMemory": 8,
          "hlaminer.runHlaMiner.timeout": 20
        },
        "description": "HLAminer workflow test",
        "engineArguments": {
           "write_to_cache": false,
           "read_from_cache": false
        },
        "id": "hlaminer_test",
        "metadata": {
            "hlaminer.resultFile": {
                "contents": [
                    {
                        "outputDirectory": "@SCRATCH@/@DATE@_Workflow_hlaminer_hlaminer_test_@JENKINSID@"
                    }
                ],
                "type": "ALL"
            },
            "hlaminer.logFile": {
                "contents": [
                    {
                        "outputDirectory": "@SCRATCH@/@DATE@_Workflow_hlaminer_hlaminer_test_@JENKINSID@"
                    }
                ],
                "type": "ALL"
            }
        },
        "validators": [
            {
                "metrics_calculate": "@CHECKOUT@/tests/calculate.sh",
                "metrics_compare": "@CHECKOUT@/tests/compare.sh",
                "output_metrics": "/.mounts/labs/gsi/testdata/hlaminer/output_metrics/hlaminer_test2.metrics",
                "type": "script"
            }
        ]
    }
]