Chapter 7 - giving snakemake filenames instead of rule names

Let's add a new genome into the mix, and start by generating a sketch file (ending in .sig) for it.

Download the RefSeq assembly file (the _genomic.fna.gz file) for GCF_008423265.1 from this NCBI link, and put it in the genomes/ subdirectory as GCF_008423265.1.fna.gz. (You can also download a saved copy with the right name from this osf.io link).

Now, we'd like to build a sketch by running sourmash sketch dna (via snakemake).

Do we need to add anything to the Snakefile to do this? No, no we don't!

To build a sketch for this new genome, you can just ask snakemake to make the right filename like so:

snakemake -j 1 GCF_008423265.1.fna.gz.sig

Why does this work? It works because we have a generic wildcard rule for building .sig files from files in genomes/!

When you ask snakemake to build that filename, it looks through all the output blocks for its rules, and choose the rule with matching output - importantly, this rule can have wildcards, and if it does, it extracts the wildcard from the filename!

Warning: the sketch_genome rule has now changed!

As a side note, you can no longer ask snakemake to run the rule by its name, sketch_genome - this is because the rule needs to fill in the wildcard, and it can't know what {accession} should be without us giving it the filename.

If you try running snakemake -j 1 sketch_genome, you'll get the following error: >WorkflowError: >Target rules may not contain wildcards. Please specify concrete files or a rule without wildcards at the command line, or have a rule without wildcards at the very top of your workflow (e.g. the typical "rule all" which just collects all results you want to generate in the end).

This is telling you that snakemake doesn't know how to fill in the wildcard (and giving you some suggestions as to how you might do that, which we'll explore below).

In this chapter we didn't need to modify the Snakefile at all to make use of new functionality!