refactor: merge prepare, map & quantify workflows

Closes #25 (closed)

• trigger workflows prepare.smk, map.smk and quantify.smk from a single Snakefile
• the separation over three files is conserved; each file is imported in the Snakefile
• use a single config.yaml file to trigger the entire run (preparation, mapping & quantification)

test/config_prepare.yaml

----
-#### GLOBAL PARAMETERS #####
-
-# Directories
-# Usually there is no need to change these
-output_dir: "results"
-scripts_dir: "../scripts"
-local_log: "logs/local"
-cluster_log: "logs/cluster"
-
-# Isomirs annotation file
-# Number of base pairs to add/substract from 5' (start) and 3' (end) coordinates.
-bp_5p: [-1, 0, +1]
-bp_3p: [-1, 0, +1]
-
-# List of inputs
-organism: ["homo_sapiens/chrY"]
-
-#### PARAMETERS SPECIFIC TO INPUTS #####
-
-homo_sapiens/chrY:
-  # URLs to genome, gene & miRNA annotations
-  genome_url: "ftp://ftp.ensembl.org/pub/release-98/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.chromosome.Y.fa.gz"
-  gtf_url: "ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/Homo_sapiens.GRCh38.98.gtf.gz"
-  mirna_url: "https://www.mirbase.org/ftp/CURRENT/genomes/hsa.gff3"
-
-  # Chromosome name mappings between UCSC <-> Ensembl
-  # Other organisms available at: https://github.com/dpryan79/ChromosomeMappings
-  map_chr_url: "https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh38_UCSC2ensembl.txt"
-  # Chromosome name mapping parameters:
-  column: 1
-  delimiter: "TAB"
-...