tldr/pages/common/nextflow.md

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2019-09-16 10:11:05 +01:00
# nextflow
> Tool for running computational pipelines. Mostly used for bioinformatics workflows.
> Homepage: <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`