We’ve so far been working with a relatively non-generalised workflow: it’s got hard-coded inputs, paths and genome references. This is perfectly fine for a project that is purely aimed at getting reproducible results (which is the full extent of what you want in a lot of cases), but it can be made a lot more generalisable. Let’s go through the MRSA workflow and see what can be improved!

Parameters

One of the things that allow generalisability of Nextflow workflows is parameters, which hold information and values that can be changed directly on the command-line at the time of execution. One use of parameters in our MRSA workflow is to remove the hard-coded results output directory, for example. Parameters can be written in the following form:

params {
    parameter_1 = "some/data/path"      // A string parameter
    parameter_2 = 42                    // A value parameter
    parameter_3 = ["a", "b", "c", "d"]  // A list parameter
}

You would then refer to these parameters using e.g. params.parameter_1 anywhere you need to in the workflow. Although parameters can be defined in main_mrsa.nf, it is preferable to define them in a separate configuration file. The default name of this file is nextflow.config and if such a file is present it will be used automatically by Nextflow (to supply a config file with another name use nextflow -c <path-to-config-file> run main_mrsa.nf)

• Create a configuration file and add a parameter for the results output directory.

• Use your newly created parameter in the publishDir directory of a process Run your workflow to see if it worked; click below if you need help.

// Configuration file
params {
    outdir = "results"
}

// A publishDir directive in a process
publishDir "${params.outdir}",
    mode: "copy"

Command line parameters

Workflow parameters can be assigned on the command-line by executing workflows like so: nextflow run main_mrsa.nf --parameter_name 'some_value'. The workflow parameter parameter_name is prefixed by a double dash -- to tell Nextflow this is a parameter to the workflow (a single dash is a parameter to Nextflow, e.g. -resume). The value is also quoted (this is important for parameters that take file paths as values).

• Run your workflow using the parameter you previously created, but pick something other than the default value!

You should now have a new directory containing all the results! This is highly useful if you want to keep track of separate runs of a workflow with different software parameters, for example: nextflow run main.nf --important_param 'value1' --resultsdir 'results-value1', or simply want to keep the results of separate versions of the same workflow. You can also change parameters by using the -params-file option or by using another configuration file (and using -c), rather than on the command line!

Configuring inputs

Remember the input for the MRSA workflow, the ch_input channel? This input (the samplesheet.csv file) is hard-coded inside the main_mrsa.nf file. This could also be made into a parameter!

• Change the definition of the ch_input channel to take the value of a new parameter of your choice, defined in the configuration file.

You should now have a more generalised input to your workflow! Try to run it to make sure it works - look below if you need some help.

// Channel definition
ch_input = Channel
    .fromPath ( params.input )
    .splitCsv ( header: true )

// Configuration file
input = "samplesheet.csv"

By specifying inputs from sample sheets like this we can change inputs of a workflow execution by creating another sample sheet and specifying e.g., --input samplesheet-2.csv on the command line. This is highly useful when you want to run a single sample e.g., when testing a workflow, or when you want to keep track of all the different inputs you’ve used historically.

Other configuration scopes

There are lots of things that you might want to add to your configuration, not just parameters! The workflow manifest, for example, which might look like this:

manifest {
    name        = "My Workflow"
    description = "My awesome workflow, created by me"
    author      = "Me"
    mainScript  = "main.nf"
    version     = "1.0.0"
}

• Go ahead and add a workflow manifest to your nextflow.config file!

The manifest is useful when you’re publishing or sharing the workflow through e.g. GitHub or similar. There are many more such configuration scopes that you might want to use - read more about them in the documentation Links to an external site..

Quick recap
In this section we learnt:

• How to create parameters in a configuration file
• How to specify parameters on the command line
• How to add workflow manifest and other configuration scopes