How to use the command 'nextflow' (with examples)

Nextflow is a powerful application that enables the execution of complex computational pipelines, primarily used in the field of bioinformatics. Built with the aim of simplifying the publishing of analysis pipelines, Nextflow allows users to write parallel workflows in a concise and portable manner. It supports execution in different computational environments, including local systems, cloud infrastructures, and high-performance computing clusters. Additionally, Nextflow includes features like workflow reproducibility, scalable parallel execution, and seamless integration with Git-based repositories.

Use case 1: Run a pipeline, use cached results from previous runs

Code:

nextflow run main.nf -resume

Motivation:

Running computational pipelines can be resource-intensive and time-consuming. Often, changes made to a workflow don’t necessitate recomputing the entire dataset but only a subset. Using the cached results from previous runs allows for efficient reuse of results, saving both time and computational resources. This feature is critical when workflows have checkpoints or when dealing with iterative development or debugging.

Explanation:

• nextflow run main.nf: This instructs Nextflow to run the pipeline specified by the main.nf script. The main.nf file typically contains the definition of the workflow tasks and their dependencies.
• -resume: This flag tells Nextflow to reuse previously computed results (cached data). If parts of the workflow have not changed, Nextflow will avoid re-running those tasks and use the cached outputs instead.

Example Output:

When running this command, users will see logs indicating cached data utilization. For instance, they might see messages like:

[cached] process > task_name [100%]

This shows that the task was retrieved from cache instead of being re-executed.

Use case 2: Run a specific release of a remote workflow from GitHub

Code:

nextflow run user/repo -revision release_tag

Motivation:

Using a specific release of a workflow ensures consistency and reproducibility across different runs. In collaborative environments or when following published work, it’s essential to use the exact version of a pipeline as it was originally intended. This approach helps in verifying results, peer reviews, or collaborative research where specific pipeline versions need to be used.

Explanation:

• nextflow run user/repo: This command starts executing a workflow hosted on GitHub. user and repo denote the GitHub username and repository name, respectively.
• -revision release_tag: The -revision option specifies a particular Git tag, branch, or commit hash in the repository. release_tag ensures that a specific version or release of the workflow is used, allowing for consistency and repeatability.

Example Output:

The console will display the nextflow process loading the specified revision, similar to:

Checking out revision 'release_tag' from repository 'user/repo'

This indicates the workflow is being sourced from the correct version.

Use case 3: Run with a given work directory for intermediate files, save execution report

Code:

nextflow run workflow -work-dir path/to/directory -with-report report.html

Motivation:

Designating a specific work directory provides better management of intermediate files generated during the execution of a workflow. This organization is crucial in maintaining orderly workflows, especially when dealing with large datasets or when storage is a constraint. Moreover, saving an execution report is beneficial for audit purposes, debugging, and tracking workflow performance.

Explanation:

• nextflow run workflow: Executes the specified workflow.
• -work-dir path/to/directory: Directs Nextflow to store all intermediate files generated during the workflow execution to the provided directory path, path/to/directory.
• -with-report report.html: Tells Nextflow to create an HTML report named report.html. This report summarizes the execution, including resource usage, runtime, and other valuable metadata.

Example Output:

The workflow will execute with any temporary files placed in the specified directory. Upon completion, you’ll find the report.html file containing a detailed report of the run.

Execution report saved as 'report.html'

Use case 4: Show details of previous runs in current directory

Code:

nextflow log

Motivation:

Monitoring and auditing past workflow executions are essential for efficient pipeline management. By checking the logs of previous runs, users can quickly assess successful runs, diagnose failed attempts, or analyze execution trends over time. This helps in optimizing workflow configurations and understanding historical data processing.

Explanation:

• nextflow log: When executed, this command queries the history of pipeline executions performed in the current workspace, providing a log with information about past workflow runs such as timestamps, statuses, and durations.

Example Output:

The command will list a history of runs similar to the following:

Date               Pipeline                  Status     Duration
2023-07-01 14:33   main.nf                   SUCCESS    43m
2023-07-02 10:07   main.nf -revision v1.0    FAILED     5m

Use case 5: Remove cache and intermediate files for a specific run

Code:

nextflow clean -force run_name

Motivation:

Periodically cleaning up cache and intermediate files for specific runs is necessary to reclaim storage space and maintain an uncluttered working environment. Especially in high-throughput environments, leftover data from past executions can take up considerable storage, impacting resource availability.

Explanation:

• nextflow clean: Initiates the cleaning process for cache and intermediate files generated by a specified run.
• -force: Forces the deletion process without requiring additional confirmation, ensuring that files are immediately removed.
• run_name: Specifies the exact pipeline run id you wish to clean up, targeting only its associated data for deletion.

Example Output:

Successful execution will show an output message like:

Cleaning run 'run_name' - 54 files removed

Use case 6: List all downloaded projects

Code:

nextflow list

Motivation:

Being able to quickly list all downloaded workflow projects aids in managing available resources, familiarity with various installed pipelines, and ensuring that necessary workflows are pre-fetched for offline or isolated environments. This navigation and discovery function streamlines organizing workflow resources.

Explanation:

• nextflow list: Command to retrieve and display all workflow projects that have been downloaded and are available locally. This provides a comprehensive list for quick access and management.

Example Output:

Upon execution, it will list available projects:

INDEX  NAME             VERSION                 DESCRIPTION
1      nexflow-one      1.2.3                   Genetic analysis
2      nexflow-two      2.1.0                   Protein modeling

Use case 7: Pull the latest version of a remote workflow from Bitbucket

Code:

nextflow pull user/repo -hub bitbucket

Motivation:

Pulling the latest versions of remote workflows ensures users are working with up-to-date processes, incorporating the newest improvements, bug fixes, and features. Keeping the workflow pipeline updated is critical for reliability and harnessing new efficiencies.

Explanation:

• nextflow pull user/repo: Fetches the latest updates from a remote workflow, with user/repo denoting the user’s repository on Bitbucket.
• -hub bitbucket: Designates Bitbucket as the source control platform, rather than the default GitHub, instructing Nextflow to interact with Bitbucket hosting services.

Example Output:

The expected output would show a successful update if newer versions are available:

Pulling nextflow scripts from 'user/repo' @ bitbucket

Use case 8: Update Nextflow

Code:

nextflow self-update

Motivation:

Regularly updating Nextflow to the latest version is essential to ensure that you are enjoying the latest features, optimizations, and security fixes. An up-to-date installation guarantees compatibility with newer workflows and enhancements from the developer community.

Explanation:

• nextflow self-update: This command checks for the latest version of Nextflow and updates your local installation automatically if it detects a newer version, simplifying maintenance and ensuring you have the latest features.

Example Output:

When successfully updated, you’ll receive confirmation in the output:

Nextflow updated to version 21.10.6

Conclusion:

Nextflow offers a robust framework for streamlining the execution of computational workflows, crucial for bioinformatics and scientific research involving complex data processing pipelines. By leveraging Nextflow’s capabilities such as pipeline caching, version control integration, report generation, and more, users can manage and optimize their analytical workflows efficiently with reproducibility and scalability. These examples illustrate how various Nextflow commands cater to different practical needs, promoting an adaptable and performance-oriented approach to scientific computing.