Configuration file¶

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When a pipeline script is launched Nextflow looks for a file named nextflow.config in the current directory andin the script base directory (if it is not the same as the current directory). Finally it checks for the file$HOME/.nextflow/config.

When more than one of the above files exist they are merged, so that the settings in the first override the same onesthat may appear in the second one, and so on.

The default config file search mechanism can be extended proving an extra configuration file by using the command lineoption -c<configfile>.

Note

It’s worth noting that by doing this, the files nextflow.config and $HOME/.nextflow/config are notignored and they are merged as explained above.

Tip

If you want to ignore any default configuration files and use only the custom one use the command line option-C<configfile>.

Config syntax¶

A Nextflow configuration file is a simple text file containing a set of properties defined using the syntax:

Please note, string values need to be wrapped in quotation characters while numbers and boolean values (true, false) do not.Also note that values are typed, meaning for example that, 1 is different from '1', since the first is interpretedas the number one, while the latter is interpreted as a string value.

Config Variables¶

Configuration properties can be used as variables in the configuration file itself, by using the usual$propertyName or ${expression} syntax.

For example:

Please note, the usual rules for String interpolation are applied, thus a string containing a variablereference must be wrapped in double-quote chars instead of single-quote chars.

The same mechanism allows you to access environment variables defined in the hosting system. Any variable whose name isnot defined in the Nextflow configuration file(s) is supposed to be a reference to an environment variable with that name.So, in the above example the property customPath is defined as the current system PATH to whichthe string /my/app/folder is appended.

Config comments¶

Configuration files use the same conventions for comments used by the Groovy or Java programming languages. Thus, use // to commenta single line or /* . */ to comment a block on multiple lines.

Config include¶

A configuration file can include one or more configuration files using the keyword includeConfig. For example:

When a relative path is used, it is resolved against the actual location of the including file.

Config scopes¶

Configuration settings can be organized in different scopes by dot prefixing the property names with a scopeidentifier or grouping the properties in the same scope using the curly brackets notation. This is shown in thefollowing example:

Scope env¶

The env scope allows the definition one or more variable that will be exported in the environment where theworkflow tasks will be executed.

Simply prefix your variable names with the env scope or surround them by curly brackets, as shown below:

Scope params¶

The params scope allows you to define parameters that will be accessible in the pipeline script. Simply prefix theparameter names with the params scope or surround them by curly brackets, as shown below:

Scope process¶

The process configuration scope allows you to provide the default configuration for the processes in your pipeline.

You can specify here any property described in the process directive and the executor sections.For examples:

By using this configuration all processes in your pipeline will be executed through the SGE cluster, with the specifiedsettings.

Process selectors¶

The withLabel selectors allow the configuration of all processes annotated with a label directive asshown below:

The above configuration example assigns 16 cpus, 64 Gb of memory and the long queue to all processes annotatedwith the big_mem label.

In the same manner, the withName selector allows the configuration of a specific process in your pipeline by its name.For example:

Tip

Either label and process names do not need to be enclosed with quote characters, provided the namedoes include special characters (e.g. -, !, etc) or it’s not a keyword or a built-in type identifier.In case of doubt, you can enclose the label names or the process names with single or double quote characters.

Selector expressions¶

Both label and process name selectors allow the use of a regular expression in order to apply the same configurationto all processes matching the specified pattern condition. For example:

The above configuration snippet sets 2 cpus and 4 GB of memory to the processes annotated with with a label fooand bar.

A process selector can be negated prefixing it with the special character !. For example:

The above configuration snippet sets 2 cpus for the processes annotated with the foo label and 4 cpus to all processesnot annotated with that label. Finally it sets the use of long queue to all process whose name does not startwith align.

Selectors priority¶

When mixing generic process configuration and selectors the following priority rules are applied (from lower to higher):

Process generic configuration.
Process specific directive defined in the workflow script.
withLabel selector definition.
withName selector definition.

For example:

Using the above configuration snippet, all workflow processes use 4 cpus if not otherwise specified in the workflowscript. Moreover processes annotated with the foo label use 8 cpus. Finally the process named baruses 32 cpus.

Scope executor¶

The executor configuration scope allows you to set the optional executor settings, listed in the following table.

Name	Description
name	The name of the executor to be used e.g. `local`, `sge`, etc.
queueSize	The number of tasks the executor will handle in a parallel manner (default: `100`).
pollInterval	Determines how often a poll occurs to check for a process termination.
dumpInterval	Determines how often the executor status is written in the application log file (default: `5min`

2021.11