run_qc.py: fix incorrect default for --split-fastqs-by-lane #923
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…ical Illumina Fastq names.
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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-laneoption) 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.pyutility) currently can't handle the resulting names when the Fastqs are split (issue #924).