nextflow run <project name, repository url, or local path>

Execute a pipeline project

Arguments

NameDescription
project name, repository url, or local path

Options

NameDescription
-EExports all current system environment (Default: false)
-ansi-logEnable/disable ANSI console logging
-bucket-dir <remote bucket>Remote bucket where intermediate result files are stored
-cacheEnable/disable processes caching
-disable-jobs-cancellationPrevent the cancellation of child jobs on execution termination
-dsl1Execute the workflow using DSL1 syntax (Default: false)
-dsl2Execute the workflow using DSL2 syntax (Default: false)
-dump-channelsDump channels for debugging purpose
-dump-hashesDump task hash keys for debugging purpose (Default: false)
-e. <key=value>Add the specified variable to execution environment. Syntax: -e.key=value (Default: {})
-entry <entry workflow name>Entry workflow name to be executed
-h, -helpPrint the command usage (Default: false)
-hub <service hub>Service hub where the project is hosted (Default: github)
-latestPull latest changes before run (Default: false)
-lib <library extension path>Library extension path
-main-script <script file>The script file to be executed when launching a project directory or repository
-name <name>Assign a mnemonic name to the a pipeline run
-offlineDo not check for remote project updates (Default: false)
-params-file <JSON/YAML file>Load script parameters from a JSON/YAML file
-plugins <plugins ids separated by comma>Specify the plugins to be applied for this run e.g. nf-amazon,nf-tower
-process. <key=value>Set process options. Syntax: -process.key=value (Default: {}
-profile <profile>Choose a configuration profile
-qs, -queue-size <number>Max number of processes that can be executed in parallel by each executor
-resume [session ID]Execute the script using the cached results, useful to continue executions that was stopped by an error
-r, -revision <project revision (tag/branch/hash>Revision of the project to run (either a git branch, tag or commit SHA number)
-stub-ru, -stubExecute the workflow replacing process scripts with command stubs (Default: false)
-test <name>Test a script function with the name specified
-user <username>Private repository user name
-with-charliecloudEnable process execution in a Charliecloud container runtime
-with-conda <conda .yml/.yaml file>Use the specified Conda environment package or file (must end with .yml|.yaml suffix)
-with-dag <filename, e.g. dag.dot>Create pipeline DAG file
-with-docker [a docker container image]Enable process execution in a Docker container
-N, -with-notification <email>Send a notification email on workflow completion to the specified recipients
-with-podmanEnable process execution in a Podman container
-with-report <report filename e.g. report.html>Create processes execution html report
-with-singularityEnable process execution in a Singularity container
-with-timeline <timeline filename e.g. timeline.html>Create processes execution timeline file
-with-towerMonitor workflow execution with Seqera Tower service
-with-trace <trace text filename e.g. trace.txt>Create processes execution tracing file
-with-weblog <target web URL>Send workflow status messages via HTTP to target URL
-without-dockerDisable process execution with Docker (Default: false)
-without-podmanDisable process execution in a Podman container
-w, -work-dir <work dir>Directory where intermediate result files are stored