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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: fix incorrect default for --split-fastqs-by-lane #923

Closed pjbriggs closed 7 months ago

pjbriggs commented 7 months ago

Fixes a bug in the standalone QC pipeline runner run_qc.py, whereby the option to split Fastqs by lane for the QC (i.e. the --split-fastqs-by-lane option) always defaulted to be being switched on. The fix is to change the default to off, and only enable the splitting if the option is specified on the command line.

Also adds a trap to check for non-canonical Illumina-style Fastq names when splitting is explicitly requested, as the pipeline (actually the split_fastqs.py utility) currently can't handle the resulting names when the Fastqs are split (issue #924).