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

@@ -4,7 +4,7 @@ default:
 
 before_script:
   - mamba env create --force -f environment.yml
-  - conda activate mir-pipelines
+  - conda activate mirflowz
   - echo $CONDA_DEFAULT_ENV
   - snakemake --version