run_qc.py: allow STAR index to be specified explicitly

fls-bioinformatics-core / auto_process_ngs

Scripts and utilities for automatic processing & management of Illumina NGS sequencing data.

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run_qc.py: allow STAR index to be specified explicitly #819

Closed pjbriggs closed 1 year ago

pjbriggs commented 1 year ago

Update the standalone QC pipeline utility run_qc.py by adding a new option --star-index which allows the STAR index used for mapping to be explicitly specified (similar to the existing options for 10x reference datasets).

This also includes an update to the underlying pipeline in qc/pipeline to enable a specific STAR index to be passed to the QC for a project.