Nextflow Command Examples (with examples)

Running a pipeline with cached results from previous runs

nextflow run main.nf -resume

Motivation: This command allows you to run your pipeline using cached results from previous executions. It can significantly speed up pipeline execution time by avoiding the re-computation of intermediate results that have not changed.

Explanation:

• nextflow run: This is the command to run a pipeline using Nextflow.
• main.nf: Replace this with the main script file of your pipeline.
• -resume: This flag tells Nextflow to use cached results from previous runs.

Example Output:

N E X T F L O W  ~  version 20.10.0
Launching main.nf [angry_keller] - revision: 12ca4f6095
...

Running a specific release of a remote workflow from GitHub

nextflow run user/repo -revision release_tag

Motivation: This command allows you to run a specific release of a remote workflow from GitHub. It is useful when you want to ensure reproducibility by using a specific version of the workflow.

Explanation:

• nextflow run: This is the command to run a pipeline using Nextflow.
• user/repo: Replace this with the GitHub repository name in the format username/repository.
• -revision release_tag: This flag specifies the specific release tag to run.

Example Output:

N E X T F L O W  ~  version 20.10.0
Launching user/repo [adoring_nightingale] - revision: v1.2.3
...

Running with a given work directory for intermediate files and saving execution report

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

Motivation: This command allows you to specify a custom work directory for storing intermediate files generated by the pipeline. It also enables you to save an execution report for later analysis.

Explanation:

• nextflow run: This is the command to run a pipeline using Nextflow.
• workflow: Replace this with the name of your workflow.
• -work-dir path/to/directory: This flag sets the directory for storing intermediate files.
• -with-report report.html: This flag saves an HTML execution report with the specified name.

Example Output:

N E X T F L O W  ~  version 20.10.0
Launching workflow [vibrant_kilby] - revision: 1a2b3c4d5e
Work dir: path/to/directory
...

Showing details of previous runs in the current directory

nextflow log

Motivation: This command allows you to view the details of previous pipeline runs in the current directory. It provides valuable information for troubleshooting and understanding the execution history.

Explanation:

• nextflow log: This command displays the details of previous pipeline runs.

Example Output:

Pipeline name: workflow
[List of previous run details]
Run name       : run1
Launch dir     : /path/to/launch/dir/run1
Launch time    : 2021-01-01 10:00:00
Exit status    : COMPLETED
... (more details)

Removing cache and intermediate files for a specific run

nextflow clean -force run_name

Motivation: This command allows you to remove the cache and intermediate files generated by a specific pipeline run. It is helpful when you want to start fresh or reclaim disk space.

Explanation:

• nextflow clean: This command removes cache and intermediate files.
• -force: This flag forces the removal without asking for confirmation.
• run_name: Replace this with the name of the run for which you want to clean the files.

Example Output:

Cleaned cache and files for run 'run1'

Listing all downloaded projects

nextflow list

Motivation: This command provides a list of all downloaded projects, which includes workflows and tools. It helps you keep track of the projects you have previously downloaded.

Explanation:

• nextflow list: This command lists all downloaded projects.

Example Output:

Downloaded projects:
1. workflow1
2. workflow2
...

Pulling the latest version of a remote workflow from Bitbucket

nextflow pull user/repo -hub bitbucket

Motivation: This command allows you to pull the latest version of a remote workflow from Bitbucket. It ensures that you have the most up-to-date version of the workflow before running it.

Explanation:

• nextflow pull: This command pulls the latest version of the workflow.
• user/repo: Replace this with the Bitbucket repository name in the format username/repository.
• -hub bitbucket: This flag specifies the workflow repository is from Bitbucket.

Example Output:

Fetching changes for repository 'bitbucket:user/repo'
Pull complete.

Updating Nextflow

nextflow self-update

Motivation: This command allows you to update Nextflow to the latest version. It ensures that you have the most recent features, bug fixes, and improvements.

Explanation:

• nextflow self-update: This command updates Nextflow to the latest version.

Example Output:

N E X T F L O W  ~  version 21.04.0

With these examples and explanations, you now have a solid understanding of how to use the Nextflow command and its various options. Whether you want to run pipelines with cached results, specify a work directory, clean up files, or update Nextflow itself, you have the commands at your fingertips. Happy pipeline building and executing!