nextflow

workflow orchestration tool

TLDR

Run pipeline

$ nextflow run [pipeline.nf]

Run with parameters

$ nextflow run [pipeline.nf] --input [data.txt]

Run from GitHub

$ nextflow run [user/repo]

Resume failed run

$ nextflow run [pipeline.nf] -resume

Run with Docker

$ nextflow run [pipeline.nf] -with-docker

Show pipeline info

$ nextflow info [pipeline]

List runs

$ nextflow log

SYNOPSIS

nextflow [command] [options]

DESCRIPTION

nextflow is a workflow orchestration tool. It runs data-driven computational pipelines.
The tool handles parallel execution. Supports cloud and HPC deployments.

PARAMETERS

COMMAND

Nextflow command.

run PIPELINE

Execute pipeline.

-resume

Resume from checkpoint.

-with-docker

Run in Docker containers.

info

Show pipeline info.

log

Show execution history.

--help

Display help information.

CAVEATS

Java-based. Requires Java 11+. Bioinformatics focused but general purpose.

HISTORY

Nextflow was created at CRG Barcelona for scalable, reproducible scientific workflows.