8. Groovy basic structures and idioms¶

Nextflow is a domain specific language (DSL) implemented on top of the Groovy programming language, which in turn is a super-set of the Java programming language. This means that Nextflow can run any Groovy or Java code.

You have already been using some Groovy code in the previous sections, but now it's time to learn more about it.

8.1 Printing values¶

To print something is as easy as using one of the print or println methods.

snippet.nf
println("Hello, World!")

The only difference between the two is that the println method implicitly appends a new line character to the printed string.

Tip

Parentheses for function invocations are optional. Therefore, the following syntax is also valid:

snippet.nf
println "Hello, World!"

Summary

In this step you have learned:

How to print a string to the console

8.2 Comments¶

Comments use the same syntax as C-family programming languages:

snippet.nf
// comment a single line

/*
    a comment spanning
    multiple lines
*/

Summary

In this step you have learned:

How to write comments in Groovy

8.3 Variables¶

To define a variable, simply assign a value to it:

snippet.nf
x = 1
println x

x = new java.util.Date()
println x

x = -3.1499392
println x

x = false
println x

x = "Hi"
println x

Local variables are defined using the def keyword:

snippet.nf
def x = 'foo'

The def should be always used when defining variables local to a function or a closure.

Summary

In this step you have learned:

How to define variables in Groovy

8.4 Lists¶

A List object can be defined by placing the list items in square brackets:

snippet.nf
list = [10, 20, 30, 40]

println list

You can access a given item in the list with square-bracket notation (indexes start at 0) or using the get method:

snippet.nf
list = [10, 20, 30, 40]

println list[0]
println list.get(0)

In order to get the length of a list you can use the size method:

snippet.nf
list = [10, 20, 30, 40]

println list.size()

You can use the assert keyword to test if a condition is true (similar to an if function).

Here, Groovy will print nothing if it is correct, else it will raise an AssertionError message.

snippet.nf
list = [10, 20, 30, 40]

assert list[0] == 10

Exercise

This assertion should be correct, try changing it to an incorrect one.

snippet.nf
list = [10, 20, 30, 40]

assert list[0] == 10

Solution

Your solution could look something similar to this:

snippet.nf
list = [10, 20, 30, 40]

assert list[0] == 11

You should see an error message similar to this:

Output

ERROR ~ assert list[0] == 11
   |   |
   |   10
   [10, 20, 30, 40]

Lists can also be indexed with negative indexes and reversed ranges.

snippet.nf
list = [0, 1, 2]
assert list[-1] == 2
assert list[-1..0] == list.reverse()

Info

In the last assert line you are referencing the initial list and converting this with a "shorthand" range (..), to run from the -1th element (2) to the 0th element (0).

List objects implement all methods provided by the java.util.List interface, plus the extension methods provided by Groovy.

snippet.nf
assert [1, 2, 3] << 1 == [1, 2, 3, 1]
assert [1, 2, 3] + [1] == [1, 2, 3, 1]
assert [1, 2, 3, 1] - [1] == [2, 3]
assert [1, 2, 3] * 2 == [1, 2, 3, 1, 2, 3]
assert [1, [2, 3]].flatten() == [1, 2, 3]
assert [1, 2, 3].reverse() == [3, 2, 1]
assert [1, 2, 3].collect { it + 3 } == [4, 5, 6]
assert [1, 2, 3, 1].unique().size() == 3
assert [1, 2, 3, 1].count(1) == 2
assert [1, 2, 3, 4].min() == 1
assert [1, 2, 3, 4].max() == 4
assert [1, 2, 3, 4].sum() == 10
assert [4, 2, 1, 3].sort() == [1, 2, 3, 4]
assert [4, 2, 1, 3].find { it % 2 == 0 } == 4
assert [4, 2, 1, 3].findAll { it % 2 == 0 } == [4, 2]

Summary

In this step you have learned:

How to define a list in Groovy
How to access a list item
How to apply methods
How to use the assert keyword

8.5 Maps¶

Maps are like lists that have an arbitrary key instead of an integer. Therefore, the syntax is very much aligned.

snippet.nf
map = [a: 0, b: 1, c: 2]

Maps can be accessed in a conventional square-bracket syntax or as if the key was a property of the map.

Click the icons in the code for explanations.

snippet.nf
map = [a: 0, b: 1, c: 2]

assert map['a'] == 0 // (1)!
assert map.b == 1 // (2)!
assert map.get('c') == 2 // (3)!

Using square brackets.
Using dot notation.
Using the get method.

To add data or to modify a map, the syntax is similar to adding values to a list:

snippet.nf
map = [a: 0, b: 1, c: 2]

map['a'] = 'x' // (1)!
map.b = 'y' // (2)!
map.put('c', 'z') // (3)!
assert map == [a: 'x', b: 'y', c: 'z']

Using square brackets.
Using dot notation.
Using the put method.

Map objects implement all methods provided by the java.util.Map interface, plus the extension methods provided by Groovy.

Summary

In this step you have learned:

How to define a map in Groovy
How to access and update maps

8.6 String interpolation¶

String literals can be defined by enclosing them with either single- ('') or double- ("") quotation marks.

snippet.nf
foxtype = 'quick'
foxcolor = ['b', 'r', 'o', 'w', 'n']
println "The $foxtype ${foxcolor.join()} fox"

x = 'Hello'
y = 'World'
println '$x $y'

Output

The quick brown fox
$x + $y

Info

Note the different use of $ and ${..} syntax to interpolate value expressions in a string literal. The $x variable was not expanded, as it was enclosed by single quotes.

Exercise

Modify the script above to print Hello World instead of $x + $y.

Solution

Modify println '$x $y' to println "$x $y".

snippet.nf
foxtype = 'quick'
foxcolor = ['b', 'r', 'o', 'w', 'n']
println "The $foxtype ${foxcolor.join()} fox"

x = 'Hello'
y = 'World'
println "$x $y"

Finally, string literals can also be defined using the / character as a delimiter. They are known as slashy strings and are useful for defining regular expressions and patterns, as there is no need to escape backslashes. As with double-quote strings they allow to interpolate variables prefixed with a $ character.

See the difference below:

snippet.nf
x = /tic\tac\toe/
y = 'tic\tac\toe'
z = "tic\tac\toe"

println x
println y

Output

tic\tac\toe
tic    ac    oe

Summary

In this step you have learned:

How to define string literals in Groovy
How to interpolate variables in string literals

8.7 Multi-line strings¶

A block of text that spans multiple lines can be defined by delimiting it with triple single or double quotes:

snippet.nf
text = """
    Hello there James.
    How are you today?
    """
println text

Output

Hello there James.
How are you today?

Finally, multi-line strings can also be defined with slashy strings. For example:

snippet.nf
text = /
    This is a multi-line
    slashy string!
    It's cool, isn't it?!
    /
println text

Output

This is a multi-line
slashy string!
It's cool, isn't it?!

Info

Like before, multi-line strings inside double quotes and slash characters support variable interpolation, while single-quoted multi-line strings do not.

Summary

In this step you have learned:

How to define multi-line strings in Groovy

8.8 If statement¶

The if statement uses the same syntax common in other programming languages, such as Java, C, and JavaScript.

if (< boolean expression >) {
    // true branch
}
else {
    // false branch
}

The else branch is optional. Also, the curly brackets are optional when the branch defines just a single statement.

snippet.nf
x = 1
if (x > 10)
    println 'Hello'

Output

Hello

Tip

null, empty strings, and empty collections are evaluated to false.

Therefore a statement like:

snippet.nf
list = [1, 2, 3]
if (list != null && list.size() > 0) {
    println list
}
else {
    println 'The list is empty'
}

Can be written as:

snippet.nf
list = [1, 2, 3]
if (list)
    println list
else
    println 'The list is empty'

See the Groovy-Truth for further details.

Tip

In some cases it can be useful to replace the if statement with a ternary expression (aka a conditional expression):

snippet.nf
println list ? list : 'The list is empty'

The previous statement can be further simplified using the Elvis operator:

snippet.nf
println list ?: 'The list is empty'

Exercise

Write an if statement that prints Hello if the variable x is greater than 10 and Goodbye if it is less than 10.

Solution

Your solution could look something similar to this:

snippet.nf
x = 11

if (x > 10)
    println 'Hello'
else
    println 'Goodbye'

Or this:

snippet.nf
x = 11

println x > 10 ? 'Hello' : 'Goodbye'

Summary

In this step you have learned:

How to define an if statement in Groovy
How to use the ternary operator
How to use the Elvis operator

8.9 For statement¶

The classical for loop syntax is supported:

snippet.nf
for (int i = 0; i < 3; i++) {
    println("Hello World $i")
}

Iteration over list objects is also possible using the syntax below:

snippet.nf
list = ['a', 'b', 'c']

for (String elem : list) {
    println elem
}

Summary

In this step you have learned:

How to define a for loop in Groovy

8.10 Functions¶

It is possible to define a custom function into a script:

snippet.nf
def fib(int n) {
    return n < 2 ? 1 : fib(n - 1) + fib(n - 2)
}

assert fib(10)==89

A function can take multiple arguments separating them with a comma.

The return keyword can be omitted and the function implicitly returns the value of the last evaluated expression. Also, explicit types can be omitted, though not recommended:

snippet.nf
def fact(n) {
    n > 1 ? n * fact(n - 1) : 1
}

assert fact(5) == 120

Summary

In this step you have learned:

How to define a function in Groovy

8.11 Closures¶

Closures are the Swiss army knife of Nextflow/Groovy programming. In a nutshell, a closure is a block of code that can be passed as an argument to a function.

A closure can also be used to define an anonymous function.

More formally, a closure allows the definition of functions as first-class objects.

snippet.nf
square = { it * it }

The curly brackets around the expression it * it tells the script interpreter to treat this expression as code. The it identifier is an implicit variable that represents the value that is passed to the function when it is invoked.

Once compiled, the function object is assigned to the variable square as any other variable assignment shown previously.

To invoke the closure execution use the special method call or just use the round parentheses to specify the closure parameter(s):

snippet.nf
assert square.call(5) == 25
assert square(9) == 81

As is, this may not seem interesting, but you can now pass the square function as an argument to other functions or methods. Some built-in functions take a function like this as an argument. One example is the collect method on lists:

snippet.nf
x = [1, 2, 3, 4].collect(square)
println x

Output
1	`[1, 4, 9, 16]`

By default, closures take a single parameter called it.

To give it a different name use the -> syntax. For example:

snippet.nf
square = { num -> num * num }

It’s also possible to define closures with multiple, custom-named parameters.

For example, when the method each() is applied to a map it can take a closure with two arguments, to which it passes the key-value pair for each entry in the map object. For example:

snippet.nf
printMap = { a, b -> println "$a with value $b" } // (1)!
values = ["Yue": "Wu", "Mark": "Williams", "Sudha": "Kumari"] // (2)!
values.each(printMap) // (3)!

Closure object that prints the key-value pair.
Defines a map object with three entries.
Invokes the each method passing the closure object.

Output

Yue with value Wu
Mark with value Williams
Sudha with value Kumari

A closure has two other important features.

First, it can access and modify variables in the scope where it is defined.

Second, a closure can be defined in an anonymous manner, meaning that it is not given a name, and is only defined in the place where it needs to be used.

As an example showing both these features, see the following code fragment:

snippet.nf
result = 0 // (1)!
values = ["China": 1, "India": 2, "USA": 3] // (2)!
values.keySet().each { result += values[it] } // (3)!
println result

Defines a global variable.
Defines a map object.
Invokes the each method passing the closure object which modifies the result variable.

Output

Learn more about closures in the Groovy documentation.

Summary

In this step you have learned:

How to define a closure in Groovy
How to invoke a closure

8.12 More resources¶

The complete Groovy language documentation is available at this link.

A great resource to master Apache Groovy syntax is the book: Groovy in Action.