Welcome to NGI Pipeline’s documentation!¶

NGI pipeline is a software designed to take demultiplexed Illumina flowcells and shove’em through an analysis pipeline (e.g. Piper/GATK or bcbio-nextgen).

NPI Pipeline Documentation:

Pipeline Components¶

Helper

The helper is…

Trigger

The triger is…

Engine

The engine is…

Pipeline Code Flow¶

The entrance point for the NGI pipeline is…

Source Code Documentation:

ngi_pipeline¶

ngi_pipeline package¶

Subpackages¶

ngi_pipeline.conductor package¶

Submodules¶

ngi_pipeline.conductor.classes module¶

ngi_pipeline.conductor.flowcell module¶

ngi_pipeline.conductor.launchers module¶

Module contents¶

ngi_pipeline.database package¶

Submodules¶

ngi_pipeline.database.classes module¶

ngi_pipeline.database.communicate module¶

ngi_pipeline.database.filesystem module¶

ngi_pipeline.database.local_process_tracking module¶

ngi_pipeline.database.test_classes module¶

ngi_pipeline.database.test_communicate module¶

ngi_pipeline.database.test_filesystem module¶

ngi_pipeline.database.test_local_process_tracking module¶

Module contents¶

ngi_pipeline.engines package¶

Subpackages¶

ngi_pipeline.engines.bcbio_ngi package¶

Module contents¶

ngi_pipeline.engines.piper_ngi package¶

Submodules¶

ngi_pipeline.engines.piper_ngi.database module¶

ngi_pipeline.engines.piper_ngi.local_process_tracking module¶

ngi_pipeline.engines.piper_ngi.results_parsers module¶

ngi_pipeline.engines.piper_ngi.test_database module¶

ngi_pipeline.engines.piper_ngi.utils module¶

ngi_pipeline.engines.piper_ngi.workflows module¶

Module contents¶

ngi_pipeline.engines.qc_ngi package¶

Submodules¶

ngi_pipeline.engines.qc_ngi.workflows module¶

Module contents¶

Welcome to NGI Pipeline’s documentation!¶

Pipeline Components¶

Pipeline Code Flow¶

ngi_pipeline¶

ngi_pipeline package¶

Subpackages¶

ngi_pipeline.conductor package¶

Submodules¶

ngi_pipeline.conductor.classes module¶

ngi_pipeline.conductor.flowcell module¶

ngi_pipeline.conductor.launchers module¶

Module contents¶

ngi_pipeline.database package¶

Submodules¶

ngi_pipeline.database.classes module¶

ngi_pipeline.database.communicate module¶

ngi_pipeline.database.filesystem module¶

ngi_pipeline.database.local_process_tracking module¶

ngi_pipeline.database.test_classes module¶

ngi_pipeline.database.test_communicate module¶

ngi_pipeline.database.test_filesystem module¶

ngi_pipeline.database.test_local_process_tracking module¶

Module contents¶

ngi_pipeline.engines package¶

Subpackages¶

Module contents¶

ngi_pipeline.log package¶

Submodules¶

ngi_pipeline.log.loggers module¶

Module contents¶

ngi_pipeline.server package¶

Submodules¶

ngi_pipeline.server.background module¶

ngi_pipeline.server.handlers module¶

ngi_pipeline.server.main module¶

Module contents¶

ngi_pipeline.tests package¶

Submodules¶

ngi_pipeline.tests.generate_test_data module¶

Module contents¶

ngi_pipeline.utils package¶

Submodules¶

ngi_pipeline.utils.classes module¶

ngi_pipeline.utils.config module¶

ngi_pipeline.utils.filesystem module¶

ngi_pipeline.utils.parsers module¶

ngi_pipeline.utils.test_classes module¶

ngi_pipeline.utils.test_config module¶

ngi_pipeline.utils.test_filesystem module¶

ngi_pipeline.utils.test_parsers module¶

Module contents¶

Module contents¶

Indices and tables¶