[FEATURE] Allow alignment of Illumina reads in cram_align_illumina_hic with minimap2

[sainsachiko]

Is your feature request related to a problem? Please describe

CRAM_MAP_ILLUMINA_HIC currently does not allow mapping Illumina reads with minimap2
To align reads with minimap2 in this subworkflow, CRAMALIGN_MINIMAP2ALIGNHIC module is used. This module always runs the filter_file_end.pl script, which is specific for processing Hi-C alignments

However, bwamem2 has a genome size limit. So we should enable Illumina alignment with minimap2.

Describe the solution you'd like

Either generalising the Hi-C mapping subWF, or creating a separate short-read mapping subWF for non-Hi-C reads

Describe alternatives you've considered

No response

Additional context

No response

[sainsachiko]

I am thinking of

• add one module for minimap2alignillumina (or any name can represent: minimap2 align non-Hi-C short reads)
• add one more boolean input to the subWF, let'say hic, accept true, false? Then based on that to choose if running minimap2alignillumina or minimap2alignhic

[prototaxites]

Copying my comments across:

• We already have minimap2align, which is not long-read specific so we should be able to use it with short reads already.
• We can re-name bwamem2alignhic to bwamem2align if it's not actually Hi-C specific.
• I am not sure how I feel about converting the Hi-C mapping subworkflow to a more general one - I would prefer that we have one normal short read workflow and one Hi-C mapping subworkflow. That leaves more room to extend to more Hi-C specific things in future if e.g. new aligners or tools come along.

[sainsachiko]

Thinking of future development, I agree that 2 seperate subWF is cleaner and easier.
Just one concern that these subWFs will contain pretty much similar logic, so once fixing something, it need to be done across them. Or maybe could those logics/elements be modularized somehow? 🤔