Get started¶
Requirements¶
Nextflow can be used on any POSIX compatible system (Linux, OS X, etc). It requires BASH and Java 8 (or higher) to be installed.
Windows systems may be supported using a POSIX compatibility layer like Cygwin (unverified) or, alternatively, installing it into a Linux VM using virtualization software like VirtualBox or VMware.
Installation¶
Nextflow is distributed as a self-contained executable 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 the following command in your terminal
window:
wget -qO- https://get.nextflow.io | bash
. It will create thenextflow
main executable file in the current directory. - Optionally, move the
nextflow
file to a directory accessible by your$PATH
variable (this is only required to avoid remembering and typing the full path tonextflow
each time you need to run it).
Tip
In the case you don’t have wget
installed you can use the curl
utility instead by entering
the following command: curl -s https://get.nextflow.io | bash
Your first script¶
Copy the following example into your favourite text editor and save it to a file named tutorial.nf
#!/usr/bin/env nextflow
params.str = 'Hello world!'
process splitLetters {
output:
file 'chunk_*' into letters mode flatten
"""
printf '${params.str}' | split -b 6 - chunk_
"""
}
process convertToUpper {
input:
file x from letters
output:
stdout result
"""
cat $x | tr '[a-z]' '[A-Z]'
"""
}
result.subscribe {
println it.trim()
}
This script defines two processes. The first splits a string in file chunks containing 6 characters,
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
subscribe
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 0.9.0
[warm up] executor > local
[22/7548fa] Submitted process > splitLetters (1)
[e2/008ee9] Submitted process > convertToUpper (1)
[1e/165130] Submitted process > convertToUpper (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 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 0.9.0
[warm up] executor > local
[22/7548fa] Cached process > splitLetters (1)
[d0/7b79a3] Submitted process > convertToUpper (1)
[b0/c99ef9] Submitted process > convertToUpper (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 your 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 'Hola mundo'
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 0.7.0
[warm up] executor > local
[6d/54ab39] Submitted process > splitLetters (1)
[a1/88716d] Submitted process > convertToUpper (2)
[7d/3561b6] Submitted process > convertToUpper (1)
odnu
m aloH