My current NGS workflow uses a Makefile. I wrote a tool parsing the output of make -d --dry-run and generating an input for GEPHI

see my post: http://plindenbaum.blogspot.fr/2012/11/visualizing-dependencies-of-makefile.html

Here is the ouput of an exome analysis ( 16 samples ):

https://twitter.com/yokofakun/status/278086490809040896

For a simple/small graph you can use dot http://graphviz.org/

Hi,

did you try to use visio ? it is Microsoft product it is not free. it is so easy yet so powerful but also here is a list of other tools powerful and easy as visio but it also free 5 Best Free Alternatives To Microsoft Visio

• OpenOffice/LibreOffice Draw
• Dia
• LucidChart
• Diagramly

• Pencil Project

  I hope that I was able to help.

I think that Dia (http://projects.gnome.org/dia/) is perfect and easy to use for such task.

http://creately.com is another good software for flowcharting. There are many examples and templates for flowcharts in the blog as well. Its a good visio alternative, available for all the platforms as well.

If you use GATK Queue to write your pipeline, you can add the flag -gv graph-output.dot on the cli to generate a dotfile (as in dot graph language) that can be converted to a nice PDF or PNG like so:

dot -Tpng graph-output.dot > graph.png
dot -Tpdf graph-output.dot > graph.pdf

It's great for both visualisation for presentations, and for debugging pipelines.

These two are pretty good:

https://www.draw.io/

http://drichard.org/mindmaps/

I'd recommend looking at Taverna, which will not only let you document your workflows but you can also run them and monitor the progress. The good thing about that is you can share your workflow with others. (You can also run your workflows programmatically, thereby extending them with some scripting.) Likewise, you can create and run workflows in Galaxy. There is also a project called Tavaxy (citation for that project is here) which will allow you to interchange parts of workflows from Taverna and Galaxy (I haven't used this one because you have to have a cloud account). I know you only asked about making visual representations of workflows, but it may be helpful to see what has already been created with these tools (and even better if you can actually use part of an existing workflow). If you want to keep it real simple and free, I will also recommend Dia for just drawing your workflows.

There's no single good tool for this sort of this as you may have gathered. All you can ask for is a good flowcharting tool. I'm partial to yEd (http://www.yworks.com/en/productsyedabout.html), which seems to strike a balance between power and ease of use.

my recommendation is Creately Flowchart Software for drawing any kind of flowchart. There are 100 of flowchart diagram examples and templates to be used freely. You can quickly create flowcharts using one-click-create feature. It works on all the platforms too, You can even create work flows, process flows and swim lanes with the app.