Modifying workflow to use pre-existing alignment


I would like to modify my workflow so that a file of new sequences are aligned and added to a pre-existing alignment. I know that I can do this via

augur align --existing-alignment`

but I’m unsure how to incorporate this into a workflow. I think that I need to create a custom rule file (my_profiles/my_example/my_rules.smk) and then add the following lines to my builds.yaml file (my_profiles/my_example/builds.yaml)


  • my_profiles/my_example/my_rules.smk

However I’m not really sure what should go in the my_rules.smk file. Looking at the default main_workflow.smk file, the rule “align” follows “checkpoint partition_sequences”. So if I create a new rule “align”, I’m not sure how to reference my input files correctly. It seems like I might have to skip the partitioning step, but I’m not sure how to create a rule that does that.

Or maybe I’m completely on the wrong track here…

I didn’t see anything in the documentation that addressed quite this issue so my apologies if I’ve missed it. Your advice would be very appreciated!

Hey Rebecca – we’re working on some solutions to this which should be merged into the master branch in the coming days: and I’ll try to write some documentation and check back in here once this functionality is working smoothly.

Oh great, thank you!