Overview

Teaching: 30 min
Exercises: 15 min
Questions
  • How can I abbreviate the rules in my pipeline?

Objectives
  • Use snakemake wildcards to simplify our rules.

  • Output files are a product not only of input files but of the scripts or code that created the output files.

After the exercise at the end of the previous episode, our Snakefile looked like this:

# generate summary table
rule zipf_test:
    input:  'abyss.dat', 'last.dat', 'isles.dat'
    output: 'results.txt'
    shell:  'python zipf_test.py abyss.dat isles.dat last.dat > results.txt'

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:
    input: 	'books/isles.txt'
    output: 'isles.dat'
    shell: 	'python wordcount.py books/isles.txt isles.dat'

rule count_words_abyss:
    input: 	'books/abyss.txt'
    output: 'abyss.dat'
    shell: 	'python wordcount.py books/abyss.txt abyss.dat'

rule count_words_last:
    input: 	'books/last.txt'
    output: 'last.dat'
    shell: 	'python wordcount.py books/last.txt last.dat'

Our Snakefile has a lot of duplication. For example, the names of text files and data files are repeated in many places throughout the Snakefile. Snakefiles are a form of code and, in any code, repeated code can lead to problems (e.g. we rename a data file in one part of the Snakefile but forget to rename it elsewhere).

D.R.Y. (Don’t Repeat Yourself)

In many programming languages, the bulk of the language features are there to allow the programmer to describe long-winded computational routines as short, expressive, beautiful code. Features in Python or R or Java, such as user-defined variables and functions are useful in part because they mean we don’t have to write out (or think about) all of the details over and over again. This good habit of writing things out only once is known as the “Don’t Repeat Yourself” principle or D.R.Y.

Let us set about removing some of the repetition from our Snakefile. In our zip_test rule we duplicate the data file names and the name of the results file name:

rule zipf_test:
    input:
            'abyss.dat',
            'last.dat',
            'isles.dat'
    output: 'results.txt'
    shell:  'python zipf_test.py abyss.dat isles.dat last.dat > results.txt'

Looking at the results file name first, we can replace it in the action with {output}:

rule zipf_test:
    input:  'abyss.dat', 'last.dat', 'isles.dat'
    output: 'results.txt'
    shell:  'python zipf_test.py abyss.dat isles.dat last.dat > {output}'

{output} is a Snakemake wildcard which is equivalent to the value we specified for {output}.

We can replace the dependencies in the action with {input}:

rule zipf_test:
    input:  'abyss.dat', 'last.dat', 'isles.dat'
    output: 'results.txt'
    shell:  'python zipf_test.py {input} > {output}'

{input} is another wildcard which means ‘all the dependencies of the current rule’. Again, when Make is run it will replace this variable with the dependencies.

Let’s update our text files and re-run our rule:

touch books/*.txt
snakemake results.txt

We get:

Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	count_words
	1	count_words_abyss
	1	count_words_last
	1	zipf_test
	4

rule count_words_last:
    input: books/last.txt
    output: last.dat
    jobid: 1

Finished job 1.
1 of 4 steps (25%) done

rule count_words_abyss:
    input: books/abyss.txt
    output: abyss.dat
    jobid: 2

Finished job 2.
2 of 4 steps (50%) done

rule count_words:
    input: books/isles.txt
    output: isles.dat
    jobid: 3

Finished job 3.
3 of 4 steps (75%) done

rule zipf_test:
    input: abyss.dat, last.dat, isles.dat
    output: results.txt
    jobid: 0

Finished job 0.
4 of 4 steps (100%) done

Update Dependencies

What will happen if you now execute:

touch *.dat
snakemake results.txt
  1. nothing
  2. all files recreated
  3. only .dat files recreated
  4. only results.txt recreated

Solution

4. Only results.txt recreated.

The rules for *.dat are not executed because their corresponding .txt files haven’t been modified.

If you run:

touch books/*.txt
snakemake results.txt

you will find that the .dat files as well as results.txt are recreated.

As we saw, {input} means ‘all the dependencies of the current rule’. This works well for results.txt as its action treats all the dependencies the same - as the input for the zipf_test.py script.

Rewrite .dat rules to use wildcards

Rewrite each .dat rule to use the {input} and {output} wildcards.

Handling dependencies differently

For many rules, we may want to treat some dependencies differently. For example, our rules for .dat use their first (and only) dependency specifically as the input file to wordcount.py. If we add additional dependencies (as we will soon do) then we don’t want these being passed as input files to wordcount.py as it expects only one input file to be named when it is invoked.

Snakemake provides several solutions to this. Depending on what we want to do, it’s possible to both index and name our wildcards.

We need to add wordcount.py as a dependency of each of our data files. In this case, we can use {input[0]} to refer to the first dependency, and {input[1]} to refer to the second.

rule count_words:
    input: 	'wordcount.py', 'books/isles.txt'
    output: 'isles.dat'
    shell: 	'python {input[0]} {input[1]} {output}'

Alternatively, we can name our dependencies.

rule count_words_abyss:
    input: 	
        wc='wordcount.py',
        book='books/abyss.txt'
    output: 'abyss.dat'
    shell: 	'python {input.wc} {input.book} {output}'

Let’s mark wordcount.py as updated, and re-run the pipeline.

touch wordcount.py
snakemake
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	count_words
	1	count_words_abyss
	1	zipf_test
	3

rule count_words_abyss:
    input: wordcount.py, books/abyss.txt
    output: abyss.dat
    jobid: 2

Finished job 2.
1 of 3 steps (33%) done

rule count_words:
    input: wordcount.py, books/isles.txt
    output: isles.dat
    jobid: 1

Finished job 1.
2 of 3 steps (67%) done

rule zipf_test:
    input: abyss.dat, last.dat, isles.dat
    output: results.txt
    jobid: 0

Finished job 0.
3 of 3 steps (100%) done

Notice how last.dat (which does not depend on wordcount.py) is not rebuilt. Intuitively, we should also add wordcount.py as dependency for results.txt, as the final table should be rebuilt as we remake the .dat files. However, it turns out we don’t have to! Let’s see what happens to results.txt when we update wordcount.py:

touch wordcount.py
snakemake results.txt

then we get:

Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	count_words
	1	count_words_abyss
	1	zipf_test
	3

rule count_words_abyss:
    input: wordcount.py, books/abyss.txt
    output: abyss.dat
    jobid: 2

Finished job 2.
1 of 3 steps (33%) done

rule count_words:
    input: wordcount.py, books/isles.txt
    output: isles.dat
    jobid: 1

Finished job 1.
2 of 3 steps (67%) done

rule zipf_test:
    input: abyss.dat, last.dat, isles.dat
    output: results.txt
    jobid: 0

Finished job 0.
3 of 3 steps (100%) done

The whole pipeline is triggered, even the creation of the results.txt file! To understand this, note that according to the dependency figure, results.txt depends on the .dat files. The update of wordcount.py triggers an update of the *.dat files. Thus, make sees that the dependencies (the .dat files) are newer than the target file (results.txt) and thus it recreates results.txt. This is an example of the power of make: updating a subset of the files in the pipeline triggers rerunning the appropriate downstream steps.

Updating One Input File

What will happen if you now execute:

touch books/last.txt
make results.txt
  1. only last.dat is recreated
  2. all .dat files are recreated
  3. only last.dat and results.txt are recreated
  4. all .dat and results.txt are recreated

More dependencies…

Add zipf_test.py as a dependency of results.txt Which method do you prefer here, indexing or named input files? Yes, this will be clunky, but we’ll fix that part later! Remember that you can do a dry run with snakemake -n -p!

Key Points