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

Closed pjbriggs closed 7 months ago

pjbriggs commented 7 months ago

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.