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)

.gitlab-ci.yml

-# default:
-#   tags:
-#     - shell
-#
-# before_script:
-#   - mamba env create --force -f environment.yml
-#   - conda activate mirflowz
-#   - echo $CONDA_DEFAULT_ENV
-#   - snakemake --version
-#
-# test:
-#   script:
-#     - bash test/test_workflow_local.sh
-#     - bash test/test_dag.sh
-#     - bash test/test_rule_graph.sh
-#
-# after_script:
-#   - bash test/test_cleanup.sh