Update to use Nextflow pipelines bacQC-ONT and assembleBAC-ONT

[tavareshugo]

Need to change the assembly section to use this instead:

https://github.com/avantonder/assembleBAC-ONT

[tavareshugo]

Test the pipeline and see if the outputs are all there for the exercises

[tavareshugo]

Updates needed:

• section 6 preparing data should use samplesheet
• section 7 read content should use bacQC-ONT
• section 8 assembly should use assembleBAC-ONT
• section 9 assembly quality revise to match output of assembleBAC
• section 11 MLST revise to match output of assembleBAC
• update slides corresponding to all those sections
• (optional) Microreact instead of FigTree