nf-core/mag improvements

Edit

Goal

Improvements to the nf-core/mag pipeline.

Description

The developers of nf-core/mag list several tools that could be added to this pipeline (see nf-core/mag#1022), as well as potential replacements — for example, QUAST is currently overkill and generates tons of useless files. I’m but a humble recent contributor to that pipeline, and a novice at Nextflow, but I’d love to work on this with other motivated people.

Hackathon attendees could choose which of these to work on and tackle some of them. There is also a discussion to be had regarding the feasibility and pertinence of an additional entry point (providing bins directly, for bin refinement), but this would require experienced Nextflow developers, which I cannot say that I am!

Tasks

• Pick tools from nf-core/mag#1022 to add to the pipeline. For example, these all already have an nf-core module published:
  • Adding the BAKTA modules as a new annotation tool alternative to Prokka
  • Adding the binette module, as a (yet another) new binner option
  • Adding the fairy modules as a superfast substitute for coverage calculation
  • Adding the myloasm modules as an alternative long reads assembler
• Look at replacing tools that no longer pull their weight (e.g. QUAST)
• Discuss the feasibility of an additional entry point that takes bins directly, for bin refinement