address reviewer comments for first release

[atrigila]

Address @mashehu's (thank you!!) comments from first release PR.

• Change version of nf-test
• Use setup-nf-test instead
• Update date to release date
• Change Figures in tables to Figures+captions
• Add file titles to Readme.md: such as ```csv title="samplesheet.csv"
• Replace table with figures for ordered list
• Order tools alphabetically based on the tool name
• Check assets/chr_rename_del.txt for chrX X
• Move info in DEVELOPMENT.md to CONTRIBUTING.md. Remove DEVELOPMENT.md.
• Check docs/images/Logo.svg
• Add a light-gray background to figures, otherwise the black will blend in with the background on the website in dark mode
• Fix typo in docs/images/metro/metro.py
• Check if docs/images/metro/txt2image.md is required
• Fix typos in output.md: "steps".
• Use one line per sentence in markdown. Makes the diffs a bit nicer to read.
• Explain in output.md where are tsv files located.
• Ensure consistency in VCF/vcf writing across output.md and README.md.
• Remove duplicate in MULTIQC in output.md
• Have three samples in usage.md instead of 6.
• Check grammar and typos in usage.md.
• Remove info described several times in usage.md.
• Give each of the tools a higher level heading, so that they appear on the ToC on the right, which might make it easier to navigate.
• Add groovy in Custom Tool Arguments section
• Remove modules/local/*/tags.yml
• Check indentation in nextflow.config
• Remove pattern checking in boolean values (rename_chr and compute_freq)
• Add a pattern checking for a comma separated list (ask for clarification on this requirement)
• Remove pattern in maximal number of individuals per batch for imputation.
• Add 0 in Minimum genotype likelihood probability P(G|R) in validation data.

[atrigila]

I will continue addressing these changes tomorrow

[atrigila]

The update to release date will be done once all changes are merged and reviewers approve the final release PR

[LouisLeNezet]

The metro map is really nice to understand which tools are used when.
We can improve it in the future if we want.