mirror of https://github.com/CrimsonTome/tldr.git
37 lines
899 B
Markdown
37 lines
899 B
Markdown
# nextflow
|
|
|
|
> Tool for running 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`
|