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
+# 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