Even more functionality in the Flagged alignment wizard

[Nicklas Nordborg]

See #1050.

• Implement possibility to flag and add/modify comments when scheduling re-extractions. Since it takes about a week or more to get the result it is good to be able keep some information about why the re-extraction was made in the first place.

• Introduce a DoNotUse flag that should be set on the top-most item that is considered incorrect. The top-most item is typically a Specimen, Lysate, RNA or Library. The flag should then be copied downstreams to all child items. A DoNotUseComment that goes along with the flag is probably also a good idea.

• Alignments that are flagged as DoNotUse should be removed from the Flagged alignments list and disabled for future genotype checks. Remaining items in the list should be checked again and items that no longer get any genotype warning should also be removed.

• A lot of other wizards need to be updated to check the DoNotUse flag. For example:
  • When manually selecting RNA for library preparation a warning should be displayed.
  • Demuxing should skip flagged libraries. The rules for generating warnings, etc. need to be updated.
  • and more...

[Nicklas Nordborg]

Copied to ticket description.