Add unicycler

[sjackman]

No description provided.

[codecov-io]

Codecov Report

Merging #156 into dev will increase coverage by 0.06%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##              dev     #156      +/-   ##
==========================================
+ Coverage   43.26%   43.33%   +0.06%     
==========================================
  Files          63       63              
  Lines        5878     5885       +7     
==========================================
+ Hits         2543     2550       +7     
  Misses       3335     3335

Impacted Files	Coverage Δ
flowcraft/generator/engine.py	90.96% <ø> (ø)	⬆️
flowcraft/generator/components/assembly.py	100% <100%> (ø)	⬆️

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[ODiogoSilva]

You're on a roll! 😄

[ODiogoSilva]

Ah, could you just update the changelog.md with the new component?

[jacarrico]

Just a note: Unicycler uses several modules such as spades correct?
Ideally, Unicycler should be also be broken down in components and be represented as a FlowCraft recipe . Am I correct ?

[sjackman]

Just a note: Unicycler uses several modules such as spades correct?

Correct. The stages for short-read assembly are…

1. Correct reads with SPAdes
2. Assemble reads with SPAdes at multiple values of k, and choose the best assembly
3. Estimate copy number of unitigs
4. Clean the assembly graph
5. Apply SPAdes repeat resolution
6. Polish the assembly with Pilon
7. Rotate circular contigs to the starting gene dnaA or repA

Ideally, Unicycler should be also be broken down in components and be represented as a FlowCraft recipe . Am I correct ?

Yep! The plan is to separate it out into the components that are separable. Unicycler is not really designed to be split up, but some steps could be separated. Read correction and polishing for example would be easy to separate.

[sjackman]

Unicycler has the options --no_correct, --no_rotate, and --no_pilon.

[sjackman]

I've added --no_correct and --no_pilon to the default options.

[sjackman]

Ah, could you just update the changelog.md with the new component?

Done. Good to go?

[sjackman]

Thanks for merging!