Major refactoring

• consistent formatting (PEP8 in most parts, also for Snakefiles, where allowed)
• change allowed sequencing modes in Snakemake input table from paired_end and single_end to pe and se, respectively
• output filenames for each rule now follow this general structure: samples/{sample_name}/{rule}/{output_file}
• remove sequencing mode from output paths for each rule; corresponding wild cards removed entirely from all rules that do not depend on sequencing mode (currently all rules that are defined in the main Snakefile in the project root directory); where absolutely necessary, sequencing mode is added as part of output file or directory instead
• remove dependency of sequencing mode for rule for FastQC; now runs separately for each strand
• change log directory structure to match the one for results
• moving and renaming outputs for MultiQC is no longer required
• code to create MultiQC custom config externalized into script scripts/rhea_multiqc_config.py
• remove rule extract_decoys_salmon; equivalent file chrName.txt produced by star_index is used instead
• add rule start which copies sample data to the results directory and enforces uniform naming
• add MultiQC output files with deterministic output to md5 sum checks performed during execution of tests/test_integration_workflow/test.{local,slurm}.sh
• refactoring of alfa rules and modification of the CI/CD test to ensure compatibility

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