example.rst

Examples

Basic pipeline

This example shows a pipeline that is made of two processes. The first process receives a FASTA formatted file and splits it into file chunks whose names start with the prefix seq_.

The process that follows, receives these files and it simply reverses their content by using the rev command line tool.

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In more detail:

• line 1: The script starts with a shebang declaration. This allows you to launch your pipeline, as any other Bash script
• line 3: Declares a pipeline parameter named params.in that is initialized with the value $HOME/sample.fa.This value can be overridden when launching the pipeline, by simply adding the option --in <value> to the script command line
• line 5: Defines a variable sequences holding a reference for the file whose name is specified by the params.in parameter
• line 6: Defines a variable SPLIT whose value is gcsplit when the script is executed on a Mac OSX or csplit when it runs on Linux. This is the name of the tool that is used to split the file.
• lines 8-20: The process that splits the provided file.
• line 10: Opens the input declaration block. The lines following this clause are interpreted as input definitions.
• line 11: Defines the process input file. This file is received from the variable sequences and will be named input.fa.
• line 13: Opens the output declaration block. Lines following this clause are interpreted as output definitions.
• line 14: Defines that the process outputs files whose names match the pattern seq_*. These files are sent over the channel records.
• lines 16-18: The actual script executed by the process to split the provided file.
• lines 22-33: Defines the second process, that receives the splits produced by the previous process and reverses their content.
• line 24: Opens the input declaration block. Lines following this clause are interpreted as input definitions.
• line 25: Defines the process input file. This file is received through the channel records.
• line 27: Opens the output declaration block. Lines following this clause are interpreted as output definitions.
• line 28: The standard output of the executed script is declared as the process output. This output is sent over the channel result.
• lines 30-32: The actual script executed by the process to reverse the content of the received files.
• line 35: Prints a result each time a new item is received on the result channel.

Tip

The above example can manage only a single file at a time. If you want to execute it for two (or more) different files you will need to launch it several times.

It is possible to modify it in such a way that it can handle any number of input files, as shown below.

In order to make the above script able to handle any number of files simply replace line 3 with the following line:

sequences = Channel.fromPath(params.in)

By doing this the sequences variable is assigned to the channel created by the :ref:`channel-path` method. This channel emits all the files that match the pattern specified by the parameter params.in.

Given that you saved the script to a file named example.nf and you have a list of FASTA files in a folder named dataset/, you can execute it by entering this command:

nextflow example.nf --in 'dataset/*.fa'

Warning

Make sure you enclose the dataset/*.fa parameter value in single-quotation characters, otherwise the Bash environment will expand the * symbol to the actual file names and the example won't work.

More examples

You can find at this link a collection of examples introducing Nextflow scripting.

Check also Awesome Nextflow for a list of pipelines developed by the Nextflow community.