diff --git a/deep_sequencing_unit/etc/service.properties b/deep_sequencing_unit/etc/service.properties index 69016c089875d9555ed17ed4574e43572ae15957..76a5c90b338f354ce7b3cdfddd9369ebfddb72a1 100644 --- a/deep_sequencing_unit/etc/service.properties +++ b/deep_sequencing_unit/etc/service.properties @@ -103,7 +103,7 @@ illumina-summary.properties-file = # Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name. # E.g. 'code-extractor' property for the thread 'my-etl' should be specified as 'my-etl.code-extractor' -inputs = flow-cell, fl1, fl2 +inputs = flow-cell, fl1, fl2, fl3, fl4, fl5, fl6, fl7, fl8 # --------------------------------------------------------------------------- # 'flow-cell' thread configuration @@ -135,7 +135,7 @@ flow-cell.data-set-info-extractor.space-code = BSSE flow-cell.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor flow-cell.type-extractor.file-format-type = PROPRIETARY flow-cell.type-extractor.locator-type = RELATIVE_LOCATION -flow-cell.type-extractor.data-set-type = FLOW_CELL +flow-cell.type-extractor.data-set-type = ILLUMINA_GA_OUTPUT flow-cell.type-extractor.is-measured = true # The storage processor (IStorageProcessor implementation) @@ -150,19 +150,78 @@ flow-cell.storage-processor.meta-data-file-prefix = PREFIX_FOR_TSV fl1.incoming-dir = targets/playground/drop-box-1 fl1.data-set-info-extractor = ch.ethz.bsse.cisd.dsu.dss.FlowLaneDataSetInfoExtractor fl1.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} -fl1.data-set-info-extractor.index-of-group-code = 0 +fl1.data-set-info-extractor.index-of-space-code = 0 fl1.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor -fl1.type-extractor.file-format-type = PROPRIETARY -fl1.type-extractor.data-set-type = FLOW_LANE +fl1.type-extractor.file-format-type = SRF +fl1.type-extractor.data-set-type = SRF_PER_LANE fl1.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor # -------- Flow Lane 2 -------------------------------------- fl2.incoming-dir = targets/playground/drop-box-2 fl2.data-set-info-extractor = ch.ethz.bsse.cisd.dsu.dss.FlowLaneDataSetInfoExtractor fl2.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} -fl2.data-set-info-extractor.index-of-group-code = 0 +fl2.data-set-info-extractor.index-of-space-code = 0 fl2.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor -fl2.type-extractor.file-format-type = PROPRIETARY -fl2.type-extractor.data-set-type = FLOW_LANE +fl2.type-extractor.file-format-type = SRF +fl2.type-extractor.data-set-type = SRF_PER_LANE fl2.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor +# -------- Flow Lane 3 -------------------------------------- +fl3.incoming-dir = targets/playground/drop-box-3 +fl3.data-set-info-extractor = ch.ethz.bsse.cisd.dsu.dss.FlowLaneDataSetInfoExtractor +fl3.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} +fl3.data-set-info-extractor.index-of-space-code = 0 +fl3.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor +fl3.type-extractor.file-format-type = SRF +fl3.type-extractor.data-set-type = SRF_PER_LANE +fl3.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor + +# -------- Flow Lane 4 -------------------------------------- +fl4.incoming-dir = targets/playground/drop-box-4 +fl4.data-set-info-extractor = ch.ethz.bsse.cisd.dsu.dss.FlowLaneDataSetInfoExtractor +fl4.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} +fl4.data-set-info-extractor.index-of-space-code = 0 +fl4.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor +fl4.type-extractor.file-format-type = SRF +fl4.type-extractor.data-set-type = SRF_PER_LANE +fl4.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor + +# -------- Flow Lane 5 -------------------------------------- +fl5.incoming-dir = targets/playground/drop-box-5 +fl5.data-set-info-extractor = ch.ethz.bsse.cisd.dsu.dss.FlowLaneDataSetInfoExtractor +fl5.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} +fl5.data-set-info-extractor.index-of-space-code = 0 +fl5.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor +fl5.type-extractor.file-format-type = SRF +fl5.type-extractor.data-set-type = SRF_PER_LANE +fl5.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor + +# -------- Flow Lane 6 -------------------------------------- +fl6.incoming-dir = targets/playground/drop-box-6 +fl6.data-set-info-extractor = ch.ethz.bsse.cisd.dsu.dss.FlowLaneDataSetInfoExtractor +fl6.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} +fl6.data-set-info-extractor.index-of-space-code = 0 +fl6.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor +fl6.type-extractor.file-format-type = SRF +fl6.type-extractor.data-set-type = SRF_PER_LANE +fl6.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor + +# -------- Flow Lane 7 -------------------------------------- +fl7.incoming-dir = targets/playground/drop-box-7 +fl7.data-set-info-extractor = ch.ethz.bsse.cisd.dsu.dss.FlowLaneDataSetInfoExtractor +fl7.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} +fl7.data-set-info-extractor.index-of-space-code = 0 +fl7.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor +fl7.type-extractor.file-format-type = SRF +fl7.type-extractor.data-set-type = SRF_PER_LANE +fl7.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor + +# -------- Flow Lane 8 -------------------------------------- +fl8.incoming-dir = targets/playground/drop-box-8 +fl8.data-set-info-extractor = ch.ethz.bsse.cisd.dsu.dss.FlowLaneDataSetInfoExtractor +fl8.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} +fl8.data-set-info-extractor.index-of-space-code = 0 +fl8.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor +fl8.type-extractor.file-format-type = SRF +fl8.type-extractor.data-set-type = SRF_PER_LANE +fl8.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor