Use separate modules for `flye` coassembly and `minigraph` before `rhea`

[ppreshant]

Goal, tasks

To take full advantage of the nextflow pipeline, we should separate the major tasks into separate modules within the genome_dynamics subworkflow before rhea.

• run the flye module with all samples under a co-assembly with --keep-haplotypes = true
• Run minigraph module to align the reads onto the gfa
  • look for a minigraph module in some nextflow pipeline (Bactopia | StrainMake etc.
• (oops, I got confused minigraph for minimap) Run nf-core/minimap_index (+_align?) module to align the reads onto the gfa
  • (found on nf-core)
• Change the metromap to reflect this (linearize pre-proc - assembly and fork reads and contigs into the other analysis branches)

References

• Note on flye params from rhea paper:

  Methods/Graph construction and coverage calculations: A single coassembly graph for the series with N samples is constructed by combining all reads from all samples into one metaFlye run (19), with --keep-haplotypes parameter set to true to maintain strain variations