Update to Innuca's recipe modules

[cimendes]

This PR updates the modules in Innuca's recipe to incorporate the latest changes in the INNUca pipeline (https://github.com/B-UMMI/INNUca). Several components where updated and/or reworked including integrity_coverage, mlst, process_assembly and process_assembly_mapping. A new component, named "insert_size" was added. I apologize for the length of the PR. They made me do it! :P

Enjoy the code review.

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This change is 

[codecov-io]

Codecov Report

Merging #191 into dev will decrease coverage by 2.37%. The diff coverage is 3.09%.

@@            Coverage Diff             @@
##              dev     #191      +/-   ##
==========================================
- Coverage   43.96%   41.59%   -2.38%     
==========================================
  Files          67       69       +2     
  Lines        6036     6404     +368     
==========================================
+ Hits         2654     2664      +10     
- Misses       3382     3740     +358

Impacted Files	Coverage Δ
flowcraft/generator/components/mlst.py	100% <ø> (ø)	:arrow_up:
flowcraft/templates/spades.py	0% <ø> (ø)	:arrow_up:
flowcraft/generator/recipes/innuca.py	100% <ø> (ø)	:arrow_up:
flowcraft/templates/integrity_coverage.py	0% <0%> (ø)	:arrow_up:
flowcraft/templates/process_assembly_mapping.py	0% <0%> (ø)	:arrow_up:
flowcraft/templates/run_mlst.py	0% <0%> (ø)
flowcraft/templates/fastqc_report.py	0% <0%> (ø)	:arrow_up:
flowcraft/templates/metaspades.py	0% <0%> (ø)	:arrow_up:
flowcraft/templates/process_assembly.py	0% <0%> (ø)	:arrow_up:
flowcraft/templates/insert_size.py	0% <0%> (ø)
... and 5 more

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