Major refactoring before release

• Add/remove rules
  • Add rules for bigWig creation
  • Remove rule extract_decoys_salmon; equivalent file chrName.txt produced by star_index is used instead
• Sequencing mode-related changes:
  • Remove sequencing mode from output paths for each rule unless absolutely necessary
  • Remove dependency of sequencing mode for rule for FastQC; now runs separately for each strand
  • Sequencing modes now referred to by pe and se rather than paired_end and single_end (new values also expected in Snakemake input table)
• Changes related to output file/directory structure & MultiQC rule
  • Output filenames for each rule now follow this general structure: samples/{sample_name}/{rule}/{output_file}
  • Moving and renaming outputs for MultiQC is no longer required
  • Code to create MultiQC custom config externalized into script scripts/rhea_multiqc_config.py
  • Add MultiQC output files with deterministic output to md5 sum checks performed during execution of tests/test_integration_workflow/test.{local,slurm}.sh
  • Change log directory structure matches results directory structure
• Changes to script scripts/labkey_to_snakemake.py
  • Clean up command line interface
  • Allow user to specify environment variables and relative paths in input table and on CLI
  • Correct faulty, remove redundant and rename some other tool-specific parameters
  • Add logging, docstrings & typing definitions
  • Restructure and comment code to improve readability; linters flake8 and mypy pass
• Miscellaneous changes
  • Consistent, PEP8-compliant formatting in most parts, including Snakemake files, where allowed
  • Add rule start which copies sample data to the results directory and enforces uniform naming
  • Refactoring of ALFA rules and modification of the CI/CD test to ensure compatibility

Closes #74 (closed), #101 (closed), #107 (closed), #108 (closed), #111 (closed), #112 (closed), #117 (closed)