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)

changed milestone to %Reevaluate quantification design

added To Do refactor labels

added 20 commits

• 343c6b8b - 1 commit from branch dev
• e02c5e7c - Upload Snakefile of the merged workflows
• 63a7dfb4 - Delete Snakefile
• 83496c92 - Add "rules" directory with the three subworkflows
• 02004840 - Snakefile of the map subworkflow
• c9a00a21 - Snakefile of the "prepare" subworkflow
• 2e3a966c - Snakefile of the "quantify" subworkflow
• ed108384 - Main snakefile (merged worflows)
• 47e2399f - Template of the config.yaml
• 1fc05e9b - Delete Snakefile
• 657972b9 - Delete Snakefile
• 02172115 - Delete Snakefile
• 0e266846 - Delete config_map.yaml
• 489f15ce - Delete config_prepare.yaml
• 0d35e6e1 - Delete config_quantify.yaml
• c848b44f - Upload "config.yaml" file for the merged workflow
• 5f7e5d53 - Replace test_workflow_local.sh
• 08ecdc9a - Replace test_workflow_slurm.sh
• 37f9af9b - Replace test_rule_graph.sh
• cb3756a1 - Replace test_dag.sh

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added 1 commit

• 1d90d9eb - simple change to trigger CI

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changed title from Resolve "Merge workflows" to refactor: merge prepare, map & quantify workflows

changed the description

added 1 commit

• e8e8dec3 - temporarily deactivate CI

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added 1 commit

• b3c38a21 - temporarily deactivate CI

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merged