Improved generation of the summary Yaml file

[priyanka-surana]

Description of feature

Update the input config to fix the summary YAML generated

[muffato]

In my tests (https://github.com/sanger-tol/blobtoolkit/issues/91#issuecomment-1936255635), this is the minimal Yaml file a user has to provide for a draft assembly

assembly:
  level: bar
settings:
  foo: 0
similarity:
  diamond_blastx:
    foo: 0
taxon:
  class: class_name
  family: family_name
  genus: genus_name
  kingdom: kingdom_name
  name: species_name
  order: order_name
  phylum: phylum_name
  superkingdom: superkingdom_name
  taxid: 0

None of the values matter, but the keys have to be present.

• The keys inside taxon: are required by the parsing library of BLOBTK_IMAGES
• Everything else is required by BLOBTOOLKIT_METADATA when making the *.metadata.yaml. The script just copies whatever content is in the input Yaml.