Long-read processing & assembly additions

[elizabethmcd]

Description of feature

Outline of long-read additions to the metagenomics-assembly-nf workflow. Inputting long reads into this workflow assumes you have already basecalled the reads using Guppy etc. Each step has one or more suggested tools listed, please add your suggestions or concerns as comments below.

• Adapter removal & QC: For adapter removal - Porechop is no longer actively maintained, Porechop_ABI appears to be the successor, Filtlong can filter reads based on quality/length
• Assembly: Flye in --meta and --nano-hq mode for nanopore reads
• Polishing: Can be a combination of medaka, racon, polypolish depending on if there are short reads to supplement with or not, how many rounds of polishing depends on error rates - can also implement an IDEEL test step to output to see how this improves with rounds of polishing
• Mapping: minimap2 for mapping to assembly

@ecpierce @Manon-Morin @taylorreiter @borgesadair1

[elizabethmcd]

Current plan and addressed in #26:

• Adapter removal with porechop_ABI
• Assembly with flye with the --meta, --nano-hq, and --scaffold flags
• Polishing options with medaka and racon for long read polishing alone, trying to keep short and long read things separate
• map with minimap2

Can also add filtlong towards the adapter removal step to filter for a certain length/quality to see if impacts the assembly

[elizabethmcd]

addressed in #26