Create new module for conciliation assembly using (fly+polishing)

[jimmlucas]

PR checklist

• [x ] This comment contains a description of changes (with reason).
• [ x] If you've fixed a bug or added code that should be tested, add tests!
• [x ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/bacass branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• [ x] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

This module can process long-reads from ONT and the method for polishing use the cover and assignment a specific number of polishing (minimap+racon) to get a better assembly and reduce the error in long-seq.

close #194
close #214

[d4straub]

Hi there!
Apologies for the late reply, somehow it seems that PR was falling through many cracks.

Thanks for this addition, I think it does benefit the pipeline.

However, there seem to be a few issues here:

• a result folder was added, but shouldnt
• local modules were added, but the corresponding nf-core modules should be used, if possible at all: FLYE, racon, seqkit rmdup
• for my personal taste there are too many empty lines

Do you feel up to modifying your PR?

[jimmlucas]

I'll working on it to fix the problems

Thanks