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Merge for version 1.0.0

Sukanya Denni requested to merge dev into main

Changed part of masterconfig.yaml: new config allows assembly of genomes with different run names, BUSCO lineages and assembly modes.

# files to run the workflow on
IDS: ["file1", "file2", "file3"]

# default mode template
  run: run1
  ploidy: 2
  busco_lineage: bacteria_odb10
  mode: default

# hi-c mode template
  run: run2
  ploidy: 2
  busco_lineage: eudicots_odb10
  mode: hi-c
  r1: path/to/r1/reads
  r2: path/to/r2/reads

# trio mode template
  run: run3
  ploidy: 2
  busco_lineage: vertebrata_odb10
  mode: trio
  p1: path/to/parent/1/reads
  p2: path/to/parent/2/reads

Regrouped workflow rules/scripts by step/theme.

Added benchmarking.

Fixed hard coded BUSCO lineage creating workflow error (issue #4 (closed) ).

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