Answers.Body: <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.sstatic.net/FSAD4.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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.sstatic.net/uTGfJ.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-12-13T08:05:38.283Z
Answers.Text: I think it's better and easier to understand to make a more concise flowchart than this, and to just publish the code along with the paper. The first flowchart seems to list every single input on which  the analysis was run. The second one is far too complex to read.
Answers.UserDisplayName: Pallie
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-12-13T09:15:34.980Z
Answers.Text: @Pallie agreed, the flowcharts can get quite complicated fast, or contain elements that you don't really need to show. You can edit them as suggested, but it would be nice to be able to display just certain parts of the pipeline in the flow chart as an option.
Answers.UserDisplayName: Whitehot
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-12-13T15:18:20.680Z
Answers.Text: Flow charts in vogue, when they are not ... reviewers are very quick to point this out
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-12-12T17:14:09.020Z
Answers.LastActivityDate: 2019-12-12T17:14:09.020Z
Answers.UserDisplayName: Chris_Rands
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-12-12T17:02:08.100Z
Comments.Text: Still waiting for the PLOS Computational biology "10 simple rules..." on this one ;)
Comments.UserDisplayName: Chris_Rands
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-12-14T16:22:51.813Z
Comments.Text: I don't know... Is a flow chart actually better than a concise description possibly divided into sections with headers and bullet points? The flow chart you linked doesn't strike me as particularly clear or informative given it takes a full page with a big figure and a wall of text. (I'm not being critical I'm genuinely asking...)
Comments.UserDisplayName: dariober
Tags: <literature>
Title: Bioinformatics flowchart for Materials and Methods
ThreadText: # Bioinformatics flowchart for Materials and Methods
  
  (Asked by: username_0 on 2019-12-12)
  
  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](https://www.researchgate.net/figure/Flowchart-of-the-main-steps-and-bioinformatics-tools-required-for-pathway-reconstruction_fig1_233751111) 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](https://bioinformatics.meta.stackexchange.com/questions/219/is-asking-about-publishing-in-bioinformatics-on-topic))
  
  **Tags:** literature
  
  > **Comments:**
  > **username_1**: Still waiting for the PLOS Computational biology "10 simple rules..." on this one ;)  
  > **username_2**: I don't know... Is a flow chart actually better than a concise description possibly divided into sections with headers and bullet points? The flow chart you linked doesn't strike me as particularly clear or informative given it takes a full page with a big figure and a wall of text. (I'm not being critical I'm genuinely asking...)  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-12-12. Score: 4
  
  If you're using a workflow management system for pipelining like [snakemake](https://snakemake.readthedocs.io/en/stable/index.html) or [ruffus](http://www.ruffus.org.uk/), you can actually build a flowchart based on the rules/functions in your code:
  
  [Snakemake example](https://snakemake.readthedocs.io/en/stable/getting_started/examples.html) with the `--dag` flag:
  
  [![enter image description here](https://i.sstatic.net/FSAD4.png)](https://i.sstatic.net/FSAD4.png)
  
  [Ruffus example](http://www.ruffus.org.uk/gallery.html) using `pipeline_printout_graph`:
  
  [![enter image description here](https://i.sstatic.net/uTGfJ.png)](https://i.sstatic.net/uTGfJ.png)
  
  You'll probably still need edit the image aftwards in software like inkscape or illustrator though.
  
  > **Comments:**
  > **username_3**: I think it's better and easier to understand to make a more concise flowchart than this, and to just publish the code along with the paper. The first flowchart seems to list every single input on which  the analysis was run. The second one is far too complex to read.  
  > **username_0**: @username_3 agreed, the flowcharts can get quite complicated fast, or contain elements that you don't really need to show. You can edit them as suggested, but it would be nice to be able to display just certain parts of the pipeline in the flow chart as an option.  
  > **username_4**: Flow charts in vogue, when they are not ... reviewers are very quick to point this out  
  
  ---
  
  