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_quantify.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"
-
-# Types of miRNAs to quantify
-#mir_list: ["miRNA", "miRNA_primary_transcript", "isomirs"]
-mir_list: ["miRNA", "miRNA_primary_transcript"]
-
-# Resources: miR annotations, chromosome name mappings
-# All of these are produced by the "prepare" workflow
-mirnas_anno: "results/homo_sapiens/chrY/mirna_filtered.bed"
-isomirs_anno: "results/homo_sapiens/chrY/isomirs_annotation.bed"
-
-# Inputs information
-input_dir: "results"
-sample: ["test_lib"]  # put all samples, separated by comma
-...