The configuration is currently done in python files contained in the config folder.
File paths should be changed or adapted there if the project is ported to a new
path.
Execute the workflow with the following command:
snakemake -pk -c 3 -n
Remove the -n flag to execute the workflow with a maximum of 3 jobs in parallel. On Windows --drop-meta can be added in case the metadata cannot be written.
Intially we set these parameters for plotting using matplotlib:
import matplotlib.pyplot as plt
import seaborn
plt.rcParams['figure.figsize'] = [4.0, 3.0]
plt.rcParams['pdf.fonttype'] = 42
plt.rcParams['ps.fonttype'] = 42
plt.rcParams['figure.dpi'] = 147
njab.plotting.set_font_sizes('x-small')
seaborn.set_style("whitegrid")snakemake --forceall --rulegraph | dot -Tpdf > rulegraph.pdf # rule graph
snakemake --forceall --rulegraph | dot -Tpng > rulegraph.png # rule graph