text: user6316: I am going to start work on the Materials and Methods for a paper I contributed to a lot in the bioinformatics processing part. I have seen some papers nowadays tend to first present the processing steps that they followed as a flow chart, to show the reader what happened generally before going into details in the written M&M section.
  Are there any specific guidelines for creating this flowchart? Do you have any tips or advice from personal experience?
  
  (I am aware that this may be off-topic. I have a meta question about it here)
  
  user104: 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.
  
original_text: 6316: <p>I am going to start work on the Materials and Methods for a paper I contributed to a lot in the bioinformatics processing part. I have seen <a href="https://www.researchgate.net/figure/Flowchart-of-the-main-steps-and-bioinformatics-tools-required-for-pathway-reconstruction_fig1_233751111" rel="nofollow noreferrer">some papers</a> nowadays tend to first present the processing steps that they followed as a flow chart, to show the reader what happened generally before going into details in the written M&amp;M section.</p>
  
  <p>Are there any specific guidelines for creating this flowchart? Do you have any tips or advice from personal experience?</p>
  
  <hr>
  
  <p>(I am aware that this may be off-topic. I have a meta question about it <a href="https://bioinformatics.meta.stackexchange.com/questions/219/is-asking-about-publishing-in-bioinformatics-on-topic">here</a>)</p>
   104: <p>If you're using a workflow management system for pipelining like <a href="https://snakemake.readthedocs.io/en/stable/index.html" rel="nofollow noreferrer">snakemake</a> or <a href="http://www.ruffus.org.uk/" rel="nofollow noreferrer">ruffus</a>, you can actually build a flowchart based on the rules/functions in your code:</p>
  
  <p><a href="https://snakemake.readthedocs.io/en/stable/getting_started/examples.html" rel="nofollow noreferrer">Snakemake example</a> with the <code>--dag</code> flag:</p>
  
  <p><a href="https://i.stack.imgur.com/FSAD4.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/FSAD4.png" alt="enter image description here"></a></p>
  
  <p><a href="http://www.ruffus.org.uk/gallery.html" rel="nofollow noreferrer">Ruffus example</a> using <code>pipeline_printout_graph</code>:</p>
  
  <p><a href="https://i.stack.imgur.com/uTGfJ.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/uTGfJ.png" alt="enter image description here"></a></p>
  
  <p>You'll probably still need edit the image aftwards in software like inkscape or illustrator though.</p>
  