fls-bioinformatics-core / auto_process_ngs

Scripts and utilities for automatic processing & management of Illumina NGS sequencing data.
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Automatically assign project-specific log directories to tasks in the QC pipeline #911

Closed pjbriggs closed 7 months ago

pjbriggs commented 8 months ago

Update the QC pipeline code in qc/pipeline.py to allow a default log directory to be defined when adding each project (via new set_default_log_dir method), which is then implicitly used when tasks are added (by overriding the add_task method of the base Pipeline class).

This allows the explicit setting of the log directory to be removed from each add_task call in the add_project and related methods, reducing the amount of boilerplate code and ensuring that any new tasks which are added in future will automatically have the correct log directory assigned.