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run_qc.py should refuse to split Fastqs by lane for non-canonical names #924

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pjbriggs opened this issue Dec 13, 2023 · 0 comments · Fixed by #923
Closed

run_qc.py should refuse to split Fastqs by lane for non-canonical names #924

pjbriggs opened this issue Dec 13, 2023 · 0 comments · Fixed by #923
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enhancement Standalone QC

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@pjbriggs
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The standalone QC runner run_qc.py should refuse to split Fastqs by lane if the input Fastqs have "non-canonical" Illumina-style names (e.g. PJB1_S1_R1_L001_001_extra_stuff.fastq.gz instead of PJB1_S1_R1_L001_001.fastq.gz).

This is because the split_fastqs.py utility can't handle non-canonical names, which messes up the reporting.
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enhancement Standalone QC
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run_qc.py: fix incorrect default for --split-fastqs-by-lane fls-bioinformatics-core/auto_process_ngs
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