The implementation is already undergoing with something similar to what is done in bacannot samplesheet.

The implementation shall go step-by-step and execution tests must be performed. A workflow will only start to be implemented when the other has been fully developed and tested.

Checklist:

short-reads only

Implement YAML samplesheet for short-reads only workflows
execute assembly with paired end reads
execute assembly with single end reads
execute assembly with both paired single end reads

long reads only

Implement YAML samplesheet for long-reads only workflows
execute assembly with nanopore reads, without nanopolish
execute assembly with nanopore reads, with nanopolish
execute assembly with pacbio reads, without gcpp
execute assembly with pacbio reads, with gcpp

Think about medaka model. It should be defined for each sample in the YAML or it must continue as a "outside-YAML" general parameter that sets the value for all samples?

Hybrid assembly

strategy 1

Implement YAML samplesheet for hybrid workflows, in strategy 1.
execute strategy one assembly with paired end reads + nanopore
execute strategy one assembly with single end reads + nanopore
execute strategy one assembly with both paired and single end reads + nanopore
execute strategy one assembly with paired end reads + pacbio
execute strategy one assembly with single end reads + pacbio
execute strategy one assembly with both paired and single end reads + pacbio

strategy 2

Implement YAML samplesheet for hybrid workflows, in strategy 2.
execute strategy two assembly with paired end reads + nanopore
execute strategy two assembly with single end reads + nanopore
execute strategy two assembly with both paired and single end reads + nanopore
execute strategy two assembly with paired end reads + pacbio
execute strategy two assembly with single end reads + pacbio
execute strategy two assembly with both paired and single end reads + pacbio

Add an option for multiple samples #15

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