CmdID

CmdID / Commands

nextflow

Run computational pipelines. tldr-pages

On several platforms

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Several platforms

from tldr-pages, CC BY 4.0

Run computational pipelines. Mostly used for bioinformatics workflows.

Run a pipeline, use cached results from previous runs

nextflow run main.nf -resumeIdentify

Run a specific release of a remote workflow from GitHub

nextflow run user/repo -revision release_tagIdentify

Run with a given work directory for intermediate files, save execution report

nextflow run workflow -work-dir path/to/directory -with-report report.htmlIdentify

Show details of previous runs in current directory

nextflow logIdentify

Remove cache and intermediate files for a specific run

nextflow clean -force run_nameIdentify

List all downloaded projects

nextflow listIdentify

Pull the latest version of a remote workflow from Bitbucket

nextflow pull user/repo -hub bitbucketIdentify

Update Nextflow

nextflow self-updateIdentify