nextflow Command Examples

Run computational pipelines. Mostly used for bioinformatics workflows. More information: https://www.nextflow.io.

• 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