-E | Exports all current system environment (Default: false) |
-ansi-log | Enable/disable ANSI console logging |
-bucket-dir <remote bucket> | Remote bucket where intermediate result files are stored |
-cache | Enable/disable processes caching |
-disable-jobs-cancellation | Prevent the cancellation of child jobs on execution termination |
-dsl1 | Execute the workflow using DSL1 syntax (Default: false) |
-dsl2 | Execute the workflow using DSL2 syntax (Default: false) |
-dump-channels | Dump channels for debugging purpose |
-dump-hashes | Dump 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, -help | Print the command usage (Default: false) |
-hub <service hub> | Service hub where the project is hosted (Default: github) |
-latest | Pull 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 |
-offline | Do 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, -stub | Execute 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-charliecloud | Enable 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-podman | Enable process execution in a Podman container |
-with-report <report filename e.g. report.html> | Create processes execution html report |
-with-singularity | Enable process execution in a Singularity container |
-with-timeline <timeline filename e.g. timeline.html> | Create processes execution timeline file |
-with-tower | Monitor 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-docker | Disable process execution with Docker (Default: false) |
-without-podman | Disable process execution in a Podman container |
-w, -work-dir <work dir> | Directory where intermediate result files are stored |