fls-bioinformatics-core / auto_process_ngs

Scripts and utilities for automatic processing & management of Illumina NGS sequencing data.
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'publish_qc': fix QC verification for projects with custom protocols #980

Closed pjbriggs closed 3 months ago

pjbriggs commented 3 months ago

Fixes a bug in the publish_qc command, when projects have used a custom QC protocol. In these cases the bug meant that QC verification would fail if the stored protocol name was not one of the built-in protocols. (Potentially it could also fail if the stored QC specification differed from that for a built-in protocol with the same name.)

The fix is to the invocation of the verify_qc function (in qc/utils.py) within the publish_qc command, to remove the explicit setting of the QC protocol from the stored name - instead verify_qc (and the underlying report_qc.py utility) is left to determine the protocol to verify against (where the QC specification will be used if present, ignoring the name).

Closes #979.