This lesson is in the early stages of development (Alpha version)

Pattern Rules


Teaching: 15 min
Exercises: 5 min
  • How can I define rules to operate on similar files?

  • Write Snakemake pattern rules.

Our Snakefile still has a ton of repeated content. The rules for each .dat file all follow a consistent pattern. We can replace these rules with a single pattern rule which can be used to build any .dat file from a .txt file in books/:

rule count_words:
    output: '{book}.dat'
    shell: 'python {input.cmd} {} {output}'

Here {book} is an arbitrary wildcard that we can use as a placeholder for any generic book to analyze. Note that we don’t have to use {book} as the name of our wildcard - it can be anything we want!

This rule can be interpreted as: “In order to build a file named [something].dat (the target) find a file named books/[that same something].txt (the dependency) and run [the dependency] [the target].”

Update your Snakefile now

Replace all your count_words rules with the given pattern rule now.

Let’s test the new pattern rule. We use the -p option to show that it is running things correctly:

snakemake -c 1 clean
snakemake -c 1 -p dats

We should see the same output as before. Note that we can still use snakemake to build individual .dat targets as before, and that our new rule will work no matter what stem is being matched.

snakemake -c 1 -p sierra.dat

which gives the output below:

Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	count_words

rule count_words:
    input:, books/sierra.txt
    output: sierra.dat
    jobid: 0
    wildcards: file=sierra

python books/sierra.txt sierra.dat
Finished job 0.
1 of 1 steps (100%) done

Using wildcards

Our arbitrary wildcards like {book} can only be used in input: and output: fields. They cannot be used directly in actions. If you need to refer to the current value of a wildcard in an action you need to qualify it with wildcards.. For example: {wildcards.file}.

Running Pattern Rules

Note that although Snakemake lets you execute a non-pattern rule by name, such as snakemake clean, you cannot execute a pattern rule this way:

snakemake -c 1 count_words
Building DAG of jobs...
Target rules may not contain wildcards. Please specify concrete files or a rule without wildcards.

As the error message indicates, you need to ask for specific files. For example, snakemake last.dat.

Our Snakefile is now much shorter and cleaner:

# generate summary table
rule zipf_test:
    input: '', 'abyss.dat', 'last.dat', 'isles.dat'
    output: 'results.txt'
    shell: 'python {input[0]} {input[1]} {input[2]} {input[3]} > {output}'

rule dats:
     input: 'isles.dat', 'abyss.dat', 'last.dat'

# delete everything so we can re-run things
rule clean:
    shell: 'rm -f *.dat results.txt'

# count words in one of our "books"
rule count_words:
    output: '{book}.dat'
    shell: 'python {input.cmd} {} {output}'

Please update your Snakefile

If you haven’t already done so, please update your Snakefile to use the single pattern rule count_words.

If we look at a graph of our workflow now, you can see that Snakemake has identified all three inputs to the count_words rule, and the value of the {book} wildcard is displayed: Dependencies represented within the Snakefile when using a pattern rule

Key Points

  • Use any named wildcard ({some_name}) as a placeholder in targets and dependencies. Snakemake will apply the pattern rule to all matching files.

  • You cannot execute pattern rules by name. You need to request specific files.

  • Wildcards can be used directly in input: and output: but not in actions. To use the current value of a wildcard in an action, prefix it with {wildcards.}.