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nextflow — Run computational pipelines. Mostly used for bioinformatics workflows. More information: <https://ww

Submitted by: @import:tldr-pages·Mar 2, 2026·

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Problem

How to use the nextflow command: Run computational pipelines. Mostly used for bioinformatics workflows. More information: <https://www.nextflow.io/docs/latest/cli.html>.

Solution

nextflow — Run computational pipelines. Mostly used for bioinformatics workflows. More information: <https://www.nextflow.io/docs/latest/cli.html>.

Run a pipeline, use cached results from previous runs:

nextflow run {{main.nf}} -resume

Run a specific release of a remote workflow from GitHub:

nextflow run {{user/repo}} -revision {{release_tag}}

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

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

Show details of previous runs in current directory:

nextflow log

Remove cache and intermediate files for a specific run:

nextflow clean -force {{run_name}}

List all downloaded projects:

nextflow list

Pull the latest version of a remote workflow from Bitbucket:

nextflow pull {{user/repo}} -hub bitbucket

Update Nextflow:

nextflow self-update

Code Snippets

Run a pipeline, use cached results from previous runs

nextflow run {{main.nf}} -resume

Run a specific release of a remote workflow from GitHub

nextflow run {{user/repo}} -revision {{release_tag}}

Run with a given work directory for intermediate files, save execution report

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

Show details of previous runs in current directory

nextflow log

Remove cache and intermediate files for a specific run

nextflow clean -force {{run_name}}

Context

tldr-pages: common/nextflow

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