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4. Adding parameters

Parameters that can be overridden, either using the command line or the Nextflow configuration file, and should be used for anything that a pipeline user may want to configure regularly.

Here, as a simple example, you will add a new parameter to your pipeline that will skip the SEQTK_TRIM process.

4.1 Default values

In the nf-core template the default values for parameters are set in the nextflow.config in the base repository.

Any new parameters should be added to the nextflow.config with a default value within the params scope.

Parameter names should be unique and easily identifiable.

Exercise

Add a new parameter skip_trim to your nextflow.config file and set it to false.

nextflow.config
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// Trimming
skip_trim                   = false

4.2 Adding parameters to your pipeline

Parameters are accessible in the pipeline script.

Here, an if statement that is depended on the skip_trim parameter can be used to control the execution of the SEQTK_TRIM process. An ! can be used to imply the logical "not".

Thus, if the skip_trim parameter is not true, the SEQTK_TRIM will be be executed.

Exercise

Add an if statement that is dependent on the skip_trim parameter to your pipeline.

workflows/mypipeline.nf
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//
// MODULE: Run SEQTK_TRIM
//
if (!params.skip_trim) {
    SEQTK_TRIM (
        ch_samplesheet
    )
    ch_trimmed  = SEQTK_TRIM.out.reads
    ch_versions = ch_versions.mix(SEQTK_TRIM.out.versions.first())
}

Now your if statement has been added to your main workflow file and has a default setting in your nextflow.config file, you will be able to flexibly skip the new trimming step using the skip_trim parameter.

Exercise

Run your pipeline with your new skip_trim parameter to check it is working:

cd /workspace/gitpod/nf-develop/
nextflow run myorg-myfirstpipeline -profile test,singularity --outdir results --skip_trim

You should see that the SEQTK_TRIM process has been skipped in your execution.

4.3 Linting your changes

Linting is a static analysis process that helps ensure code quality by automatically identifying syntax errors, potential bugs, and adherence to coding standards. By enforcing consistency and best practices, linting enhances code readability, reduces errors, and streamlines the development workflow.

As a part of nf-core tools, the nf-core pipelines lint command can be used to check for inconsistencies in your code, compare your code against source code, and compare your code against nf-core standards.

Executing the nf-core pipelines lint command from within your pipeline repository will print a list of ignored tests, warnings, failed tests, and a summary.

╭───────────────────────╮
│ LINT RESULTS SUMMARY  │
├───────────────────────┤
│ [✔] 192 Tests Passed  │
│ [?]   0 Tests Ignored │
│ [!]  29 Test Warnings │
│ [✗]   1 Test Failed   │
╰───────────────────────╯

Exercise

Lint your pipeline:

cd /workspace/gitpod/nf-develop/myorg-mypipeline
nf-core pipelines lint

It is expected some tests will fail

4.4 Updating nextflow_schema.json

If you have added parameters and they have not been documented in the nextflow_schema.json file then pipeline tests will fail during linting.

schema_params: Param skip_trim from nextflow config not found in nextflow_schema.json

For linting tests to pass the nextflow_schema.json file must be updated with the parameters that were added to your pipeline but have not been documented.

The nextflow_schema.json file can get very big and very complicated very quickly.

The nf-core pipelines schema build command is designed to support developers write, check, validate, and propose additions to your nextflow_schema.json file.

nf-core pipelines schema build

It will enable you to launch a web builder to edit this file in your web browser rather than trying to edit this file manually.

INFO     [✓] Default parameters match schema validation
INFO     [✓] Pipeline schema looks valid (found 26 params)
✨ Found 'params.skip_trim' in the pipeline config, but not in the schema. Add to pipeline schema? [y/n]: y
INFO     Writing schema with 27 params: 'nextflow_schema.json'
🚀  Launch web builder for customization and editing? [y/n]: y

Using the web builder you can add add details about your new parameters.

The parameters that you have added to your pipeline will be added to the bottom of the nf-core schema build file. Some information about these parameters will be automatically filled based on the default value from your nextflow.config. You will be able to categorize your new parameters into a group, add icons, and add descriptions for each.

Pipeline parameters

Note

Ungrouped parameters in schema will cause a warning.

Once you have made your edits you can click Finished and all changes will be automatically added to your nextflow_schema.json file.

Exercise

Execute the nf-core pipelines schema build command to update your schema.

cd /workspace/gitpod/nf-develop/myorg-mypipeline
nf-core pipelines schema build

Make sure you add the skip_trim parameter to a new or existing group to avoid creating a new warning.

Lint your pipeline again to see if the tests pass.

nf-core pipelines lint

All pipeline tests should pass.

Congratulations! You have now added a new parameter to your pipeline and updated the schema for linting tests to pass!