Update the README file

[anwarMZ]

Description of feature

Update the README

• [ ] Write the usage instructions
• [ ] instructions for the required databases (if any)
• [ ] instructions for the required containers (if any)
• [ ] Create a flowchart on draw.io and connect the editable link to this issue for group development
• [ ] Update the contributors

Note: This issue should not be closed. This is an ongoing issue that will required to be updated after every hackathon session

[anwarMZ]

• Workflow - seqqc/annotation QC - list and describe modules for each sub-workflow and highlight one or two key parameters e.g., --assembler {skesa | spades | ...} | - raw-reads-qc | - taxonomy-qc | - Assembly-qc | - Assembly Annotation | - gene-prediction | - amr | - phage | - plasmid | - CRISPR | - Pan-genome analysis

• Modes - Illumina/ nanopore QC | - raw-reads-qc-nanopore ; list and describe | - Assembly-nanopore

• Input - This would include, data formats, sample sheets (links to examples), and an example figure of input data directory structure.

• Figure - Flowchart (we can use the current version for now). Update it later

• Command line - Example minimal command for running seqqc and annotation workflows with Illumina/nanopore modes where applicable

• Future work / Continuous development In addition to adding features to the current structure, List down 1/2 sub-workflows coming later in the year. e.g., variant analysis, and phylogenetic analysis.