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nextflow

Tool for running computational pipelines. Mostly used for bioinformatics workflows.

More information.

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

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