Snakemake wildcard usage


I have a set of files that I’d like to perform a function on, with the goal of applying one or more parameters in that function that include more than one possible state.

For example, I might have two samples, each with their own fasta file: sample_A and sample_B.

I want to perform a blast search for each input fasta file, but I also want to loop through a range of word sizes for every blast process for each sample. Say, three values: 11, 13, 15.

This would mean that for the sample_*.fasta input, I’d generate three blast output files, each one reflecting one of those three word size values.

I am struggling to understand how to structure the snakemake rule for input and output names, because my they don’t share the same wildcards - there is an extra name from the blast parameter output that isn’t part of the input name.

Thanks for advice on how to include a parameter name in a snakemake rule into the output name!



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