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nextflow: Move to common (#3270)

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Phil Ewels
2019-09-17 21:46:07 +02:00
committed by Starbeamrainbowlabs
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pages/linux/nextflow.md
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# 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`