Create a better DAG file

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1

Hi there,
Thank you for this platform for nextflow.

I’m using nextflow v23.10.0.5889

I run following command:

nextflow run main.nf -params-file wes_rna_input_params.json  -with-dag flowchart.png

It generates a .dot file, I convert the dot file using graphViz’s dot executable into a .png

dot -Tpng flowchart.dot -o nextflow.png

Great so far. The graph is genrated.

However, it has all the operations printed: flatmap, collect, groupTuple, join, etc.

  1. How do I disable those operations to be shown in the graph/dot file generated?

  2. How do I create a better graph, for e.g., colored or something using R? Is that doable?

2

Hey @complexgenome

All the information about the DAG generated by Nextflow can be found in this section and in this one of the official Nextflow documentation. I recommend you export as .html to get a cooler DAG (with Mermaid :star_struck:) and set verbose to false.

But if you want to do something else, more customized, the easier way is to get the dot file, load to some programming language such as R and then you can do anything you want :wink:

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@mribeirodantas
It says the default is changed to .html from .dot file format from 23.10. However, I still get a .dot file.

4

If you don’t provide any file format, the default is HTML. For example:

nextflow run hello -with-dag filename

filename will be an HTML file. If you pass -with-dag filename.png or -with-dag filename.dot it won’t be an HTML but a PNG or DOT, depending on the extension.

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