nextflow

nextflow

TLDR

Run a pipeline, use cached results from previous runs

$ nextflow run [main.nf] -resume
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Run a specific release of a remote workflow from GitHub
$ nextflow run [user/repo] -revision [release_tag]
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Run with a given work directory for intermediate files, save execution report
$ nextflow run [workflow] -work-dir [path/to/directory] -with-report [report.html]
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Show details of previous runs in current directory
$ nextflow log
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Remove cache and intermediate files for a specific run
$ nextflow clean -force [run_name]
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List all downloaded projects
$ nextflow list
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Pull the latest version of a remote workflow from Bitbucket
$ nextflow pull [user/repo] -hub bitbucket
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Update Nextflow
$ nextflow self-update
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