Snakemake input functions

Snakemake input functions.

We will start with rule cat, which takes two files and makes a new one named all.

What cat does is take the content of the input files and stick them together in the output files.

Within the files sample_a and sample _b, we have a short declarative string.

# rule cat:
# input: "sample_a.txt", "sample_b.txt"
# output: "all.txt"
# shell: "cat {input} x {output}"

We launch the pipeline, rule cat is run, and file all is generated.

If we open the file all we see is a concatenation of the two input files.

########

So if we look at the input, we see that both files are the same except for one letter. Since this is a common occurrence, there is a built-in function in Snakemake to deal with these situations named expand.

We can use it like this.

# rule copy:
# input: expand("sample_{x}.txt", x =["a","b"])
# output: "all.txt"
# shell: "cat {input} x {output}"

When we launch the pipeline, the rule is run, and we can see that the intended shell command is generated as well as the all file.

########

An important aspect of expand is that it can take wildcards propagating from the output.

Let's make the extension of the file a wildcard, and let's name it y.

If you are not sure how wildcards work, I will encourage you to check the videos from this series on the topic. Also, we have a video explaining rule all.

# rule all:
# input: "all.txt"
#
# rule copy:
# input: expand("sample_{x}.{y}", x =["a","b"])
# output: "all.{y}"
# shell: "cat {input} x {output}"

When we launch the pipeline, it crashes with a wildcard error claiming that no values were given for wildcard y.

# WildcardError in file /Users/Marcos/Desktop/snakemake/Snakefile, line 5:
# No values given for wildcard 'y'.
# File "/Users/Marcos/Desktop/snakemake/Snakefile", line 5, in module

#########

What we need to do is indicate with a double curly bracket that the y in the input is actually the wildcard associated with the y wildcard from the input.

# rule all:
# input: "all.txt"
#
# rule copy:
# input: expand("sample_{x}.{{y}}", x=["a","b"])
# output: "all.{y}"
# shell: "cat {input} x {output}"

Now the pipeline launches, the rules are run, the shell string is well formed, and we get the all.txt file.

########

The input also admits native python functions, such as lambda. So we can write the equivalent string of input files.

Note that here we have to give wildcards as a parameter of the function.

# rule all:
# input: "all.txt"
#
# rule copy:
# input:
# lambda wildcards: \
# ["sample_" + x + "." + wildcards.y \
# for x in ["a", "b"]]
# output: "all.{y}"
# shell: "cat {input} x {output}"

We can launch the pipeline, the rules are run, the shell command is well formed, and we get the all.txt file.

##############

Actually, we can pass any function to the input to customize it as much as we want. For example, we can write an equivalent function using a for loop.

So now we need to specify that the rule input should be the function we just wrote.

# rule all:
# input: "all.txt"
#
# X = ["a", "b"]
# def the_files(wildcards):
# files=[]
# for letter in X:
# file = "sample_" + letter + "." + wildcards.y
# files = files+[file]
# return files
#
# rule copy:
# input: the_files
# output: "all.{y}"
# shell: "cat {input} x {output}"

Again the pipeline does not crash, the shell command is well formed, and we get the all.txt file as well.