Grandma's recipes

New features

• Added new recipe system to flowcraft along with 6 starting recipes.
  Recipes are pre-made and curated pipelines that address specific questions.
  To create a recipe, the -r <recipe_name> can be used. To list available
  recipes, the --recipe-list and --recipe-list-short options were added.
• Added -ft or --fetch-tags which allows to retrieve all DockerHub
  container tags.
• Added function to collect all the components from the components classes,
  replacing the current process_map dictionary implementation. Now, it will be
  generated from the engine rather than hardcoded into the dict.

Components changes

• Added new disableRR param in the spades component that disables repeat
  resolution
• The abyss and spades components emit GFA in a secondary channel.
• The new bandage component can accept either FASTA from a primary channel
  or GFA from a secondary channel.
• Updated skesa to version 2.3.0.
• Updated mash based components for the latest version - 1.6.0-1.

New components

• Added component abyss.
• Added component bandage.
• Added component unicycler.
• Added component prokka.
• Added component bcalm.
• Added component diamond.

Minor/Other changes

• Added removal of duplicate IDs from reads_download component input.
• Added seed parameter to downsample_fastq component.
• Added bacmet database to abricate component.
• Added default docker option to avoid docker permission errors.
• Changed the default URL generated by inspect and report commands.
• Added directives to -L parameter of build module.

Bug fixes

• Fixed forks with same source process name.
• Fixed inspect issue when tasks took more than a day in duration.
• Added hardware address to inpsect and report hash.