Bioinformatics flowchart for Materials and Methods
If you're using a workflow management system for pipelining like snakemake or ruffus, you can actually build a flowchart based on the rules/functions in your code:

Snakemake example with the --dag flag:



Ruffus example using pipeline_printout_graph:



You'll probably still need edit the image aftwards in software like inkscape or illustrator though.