NationalGenomicsInfrastructure/ngi_pipeline

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NameLines of codeMaintainabilityTest coverage
doc/source/api/ngi_pipeline.utils.test_classes.rst
doc/source/api/ngi_pipeline.utils.test_config.rst
doc/source/api/ngi_pipeline.utils.test_filesystem.rst
doc/source/api/ngi_pipeline.utils.test_parsers.rst
doc/source/conf.py49
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doc/source/index.rst
doc/source/introduction/codeflow.rst
doc/source/introduction/components.rst
docker/Dockerfile
docker/build_docker_and_singularity.sh
docker/conda_install.sh
docker/ngi_config.yaml
docker/singularity_ngi_pipeline.sh
milou_ngi_config.yaml
nestor_ngi_config.yaml
ngi_pipeline/__init__.py4
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ngi_pipeline/conductor/__init__.py5
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ngi_pipeline/conductor/classes.py148
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ngi_pipeline/conductor/flowcell.py365
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ngi_pipeline/conductor/launchers.py71
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ngi_pipeline/database/__init__.py1
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ngi_pipeline/database/classes.py212
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ngi_pipeline/database/communicate.py26
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ngi_pipeline/database/filesystem.py152
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ngi_pipeline/database/utils.py19
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ngi_pipeline/engines/__init__.py0
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ngi_pipeline/engines/piper_ngi/__init__.py1
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ngi_pipeline/engines/piper_ngi/command_creation_config.py115
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ngi_pipeline/engines/piper_ngi/database.py70
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ngi_pipeline/engines/piper_ngi/launchers.py370
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ngi_pipeline/engines/piper_ngi/local_process_tracking.py542
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ngi_pipeline/engines/piper_ngi/parsers.py159
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ngi_pipeline/engines/piper_ngi/utils.py397
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ngi_pipeline/engines/piper_ngi/workflows.py148
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ngi_pipeline/engines/qc_ngi/__init__.py1
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ngi_pipeline/engines/qc_ngi/launchers.py117
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ngi_pipeline/engines/qc_ngi/workflows.py204
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ngi_pipeline/engines/rna_ngi/__init__.py2
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ngi_pipeline/engines/rna_ngi/database.py47
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ngi_pipeline/engines/rna_ngi/launchers.py120
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ngi_pipeline/engines/rna_ngi/local_process_tracking.py87
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ngi_pipeline/engines/sarek/__init__.py2
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ngi_pipeline/engines/sarek/database.py301
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ngi_pipeline/engines/sarek/exceptions.py109
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ngi_pipeline/engines/sarek/launchers.py43
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ngi_pipeline/engines/sarek/local_process_tracking.py205
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ngi_pipeline/engines/sarek/models/__init__.py0
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ngi_pipeline/engines/sarek/models/resources.py120
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ngi_pipeline/engines/sarek/models/sample.py147
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ngi_pipeline/engines/sarek/models/sarek.py486
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