Get started¶

Requirements¶

Nextflow can be used on any POSIX compatible system (Linux, OS X, etc). It requires Bash 3.2 (or later) and Java 8 (or later, up to 15) to be installed.

For the execution in a cluster of computers the use a shared file system is required to allow the sharing of tasks input/output files.

Windows system is supported through WSL.

Installation¶

Nextflow is distributed as a self-installing package, which means that it does not require any special installation procedure.

It only needs two easy steps:

Download the executable package by copying and pasting either one of the following commands in your terminal window: wget -qO- https://get.nextflow.io | bash

Or, if you prefer curl: curl -s https://get.nextflow.io | bash

This will create the nextflow main executable file in the current directory.
Make the binary executable on your system by running chmod +x nextflow.
Optionally, move the nextflow file to a directory accessible by your $PATH variable (this is only required to avoid remembering and typing the full path to nextflow each time you need to run it).

Tip

Set export CAPSULE_LOG=none to make the dependency installation logs less verbose.

Note

To avoid downloading the dependencies, you could also use the nextflow-VERSION-all variant available from Github for every Nextflow release version.

Go to the Github releases page and unfold the Assets section for a release.
Copy the URL of the nextflow-VERSION-all asset and issue the download command on your terminal. wget -qO- ASSET-URL. It will create the completely self-contained nextflow-VERSION-all executable file in the current directory.

Your first script¶

Copy the following example into your favourite text editor and save it to a file named tutorial.nf

#!/usr/bin/env nextflow

params.str = 'Hello world!'

process splitLetters {

    output:
    file 'chunk_*' into letters

    """
    printf '${params.str}' | split -b 6 - chunk_
    """
}


process convertToUpper {

    input:
    file x from letters.flatten()

    output:
    stdout result

    """
    cat $x | tr '[a-z]' '[A-Z]'
    """
}

result.view { it.trim() }

This script defines two processes. The first splits a string into 6-character chunks, writing each one to a file with the prefix chunk_, and the second receives these files and transforms their contents to uppercase letters. The resulting strings are emitted on the result channel and the final output is printed by the view operator.

Execute the script by entering the following command in your terminal:

nextflow run tutorial.nf

It will output something similar to the text shown below:

N E X T F L O W  ~  version 19.04.0
executor >  local (3)
[69/c8ea4a] process > splitLetters   [100%] 1 of 1 ✔
[84/c8b7f1] process > convertToUpper [100%] 2 of 2 ✔
HELLO
WORLD!

You can see that the first process is executed once, and the second twice. Finally the result string is printed.

It’s worth noting that the process convertToUpper is executed in parallel, so there’s no guarantee that the instance processing the first split (the chunk Hello) will be executed before the one processing the second split (the chunk world!).

Thus, it is perfectly possible that you will get the final result printed out in a different order:

WORLD!
HELLO

Tip

The hexadecimal numbers, like 22/7548fa, identify the unique process execution. These numbers are also the prefix of the directories where each process is executed. You can inspect the files produced by them changing to the directory $PWD/work and using these numbers to find the process-specific execution path.

Modify and resume¶

Nextflow keeps track of all the processes executed in your pipeline. If you modify some parts of your script, only the processes that are actually changed will be re-executed. The execution of the processes that are not changed will be skipped and the cached result used instead.

This helps a lot when testing or modifying part of your pipeline without having to re-execute it from scratch.

For the sake of this tutorial, modify the convertToUpper process in the previous example, replacing the process script with the string rev $x, so that the process looks like this:

process convertToUpper {

    input:
    file x from letters

    output:
    stdout result

    """
    rev $x
    """
}

Then save the file with the same name, and execute it by adding the -resume option to the command line:

nextflow run tutorial.nf -resume

It will print output similar to this:

N E X T F L O W  ~  version 19.04.0
executor >  local (2)
[69/c8ea4a] process > splitLetters   [100%] 1 of 1, cached: 1 ✔
[d0/e94f07] process > convertToUpper [100%] 2 of 2 ✔
olleH
!dlrow

You will see that the execution of the process splitLetters is actually skipped (the process ID is the same), and its results are retrieved from the cache. The second process is executed as expected, printing the reversed strings.

Tip

The pipeline results are cached by default in the directory $PWD/work. Depending on your script, this folder can take of lot of disk space. If you are sure you won’t resume your pipeline execution, clean this folder periodically.

Pipeline parameters¶

Pipeline parameters are simply declared by prepending to a variable name the prefix params, separated by dot character. Their value can be specified on the command line by prefixing the parameter name with a double dash character, i.e. --paramName

For the sake of this tutorial, you can try to execute the previous example specifying a different input string parameter, as shown below:

nextflow run tutorial.nf --str 'Bonjour le monde'

The string specified on the command line will override the default value of the parameter. The output will look like this:

N E X T F L O W  ~  version 19.04.0
executor >  local (4)
[8b/16e7d7] process > splitLetters   [100%] 1 of 1 ✔
[eb/729772] process > convertToUpper [100%] 3 of 3 ✔
m el r
edno
uojnoB

Tip

As of version 20.11.0-edge any . (dot) character in a parameter name is interpreted as the delimiter or nested scope e.g. --foo.bar Hello will be accessible from the script as params.foo.bar. If you want to have a parameter name including a . (dot) character escape it using the back-slash character e.g. --foo\.bar Hello