summarize-multiqc-pair doesn't give information for each read pair separately anymore.

[simonleandergrimm]

@willbradshaw I didn't see an issue for this, though you noted it in the code itself:

# NB: Current paired version can't distinguish or annotate forward vs reverse reads in these plots.
# TODO: Restore this functionality (will require workflow restructuring).

This might not matter much for Illumina data, but our current test dataset is AVITI sequencing, where the forward reads have far better quality than the reverse reads, leading plots that do not take into account read quality to look very bad:

mgs-workflow/modules/local/summarizeMultiqcPair/resources/usr/bin/summarize-multiqc-pair.R

Line 76 in 8c6809d

# NB: Current paired version can't distinguish or annotate forward vs reverse reads in these plots.

[willbradshaw]

In the few cases where it matters, it should be possible for the user to distinguish forward from reverse reads based on the information in the output; e.g. based on the file column in the quality/adapter QC data.

I'm not sure what you mean by "look very bad", but if you mean the zigzag effect due to having multiple rows in the same plotting group, you can fix this in ggplot with group=file (I'm not sure what the equivalent for matplotlib is but it very likely exists).