Redesign pipeline to allow multiple samples

[HenrikSpiegel]

We need to restructure the pipeline so that multiple samples are generated.

Primary:

• [x] Increase number of samples generated per dataset (replicates?)
• [x] Ensure they are easy reachable (sample_0, sample_1, sample_2 etc)

Secondary

• [x] Update pipeline to run on all samples within dataset
• [x] Update plots to reflect replicates

[HenrikSpiegel]

The simulation pipeline has been move to run_simulation.py which runs 1 readsGB dataset at a time.

We should next work on creating the analysis pipeline part.

[HenrikSpiegel]

The plotting overview is contained in analysis/05_(...)

We should consider updating the distribution plotting 02(....)
Meanwhile 03 and 04 should be depreciated and the information is found in 05