Snakemake: dynamic + non-dynamic output

Question

I have a use case in which a rule generates an arbitrary number of "checkpoint" files and a single output file. For example, "example.input" would produce:

example_000.checkpoint
example_001.checkpoint
...
example_093.checkpoint (arbitrary number here)
example.output (guaranteed non-dynamic output)

The checkpoints are intended to be used to restart from that point in the calculation, but I have additional use for them. However, I only need the first (e.g., example_000.checkpoint) and the last (e.g., example_093.checkpoint). How can I construct a rule such that my outputs are defined as:

    rule example:
        input:
            {id}.input
        output:
            non_dynamic = {id}.output
            first = {id}_{first}.checkpoint
            last = {id}_{last}.checkpoint
            # OR
            checkpoints = dynamic({id}_{checkpoint}.checkpoint)

If I define new wildcards, I get the error "Not all output files of rule example contain the same wildcards." If I try to use dynamic output, I get the error "A rule with dynamic output may not define any non-dynamic output files."

Thanks in advance for any help!

Snakemake: dynamic + non-dynamic output

0 Answers