fastqc results don't always line up in summary file

[erinyoung]

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]

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]

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]

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

[erinyoung]

Fixed in #157