Discuss

[sjackman]

Discuss random thoughts here.

[sjackman]

assemblerflow.py assembles Nextflow pipelines of modular tools for genome assembly.
https://github.com/ODiogoSilva/assemblerflow#readme
For example

assemblerflow.py build -t "trimmomatic fastqc skesa pilon" -o my_pipeline.nf
nextflow run my_pipeline.nf --fastq path/reads.fastq

[sjackman]

Shovill is a good example of an assembly pipeline. https://github.com/tseemann/shovill#main-steps
I wonder whether the subcomponents of SPAdes could be separated.