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UPHL-BioNGS / Cecret

Reference-based consensus creation
MIT License
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fastqc results don't always line up in summary file #148

Closed erinyoung closed 1 year ago

erinyoung commented 1 year ago

If the sample name doesn't match what fastqc and multiqc thinks it should be, then the fastqc results don't get linked to the right sample in the final summary file.

This is annoying.

erinyoung commented 1 year ago

In principle, what needs to happen is some sort of file or key with the sample and corresponding fastq files that can be used for matching.

erinyoung commented 1 year ago

vadr results have similar issues (see kitchen sink test to replicate)

nextflow run ~/sandbox/Cecret \
    -profile singularity,artic_V3 \
    --reads /home/eriny/sandbox/test_files/cecret/reads \
    --single-reads /home/eriny/sandbox/test_files/cecret/single-reads \
    --fastas /home/eriny/sandbox/test_files/cecret/fastas \
    --multifastas /home/eriny/sandbox/test_files/cecret/multifasta \
    --outdir kitchen_sink  \
    -with-tower
erinyoung commented 1 year ago

FastQC results now line up, but there wasn't time to check vadr for 3.6.20230418

erinyoung commented 1 year ago

Fixed in https://github.com/UPHL-BioNGS/Cecret/pull/157