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Run computational pipelines. Mostly used for bioinformatics workflows. More information:

  • Run a pipeline, use cached results from previous runs:

nextflow run {{}} -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