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nf-core / bacass

Simple bacterial assembly and annotation pipeline
https://nf-co.re/bacass
MIT License
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Assembly Polishing is not working in the V2.0 #63

Closed varunshamanna closed 2 years ago

varunshamanna commented 3 years ago

Description of the bug

Assembly Polishing step is not being performed in the workflow by default nor with the param --polish_method

Steps to reproduce

Steps to reproduce the behaviour:

  1. Command line: nextflow run nf-core/bacass --input 'sample_sheet.csv' --outdir /data/nihr/nanopore_sequencing/9_08_21/hybrid_assembly_output/ -profile docker --assembly_type hybrid -resume --kraken2db "https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz"

Nextflow Installation

Container engine

Screenshot from 2021-08-30 16-47-10

d4straub commented 3 years ago

My notes say that assembly polishing is already done by Unicycler, that is used for hybrid assembly. Do you have there an opposing example/guideline/source? I am open to changing that, but need some sort of reference that this is beneficial.

varunshamanna commented 3 years ago

I am kind of new to nanopore analysis. I think from your code it means that assembly polishing is not required when doing the hybrid assembly. Is that right? Correct me if I am wrong. If it is so please close the issue.

d4straub commented 2 years ago

Yes, I just checked: Unicycler assembly (used for hybrid assembly) includes indeed already polishing with Pilon. So no additional polishing step is needed. I close that issue, open another one if you recognize other oddities!