{
"name": "nextflow",
"description": "Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages",
"subcommands": [
{
"name": "clean",
"description": "Clean up project cache and work directories (Default: last run)",
"options": [
{
"names": [
"-after"
],
"description": "Clean up runs executed after the specified one",
"takes_arg": true,
"arg": {
"name": "run name"
}
},
{
"names": [
"-before"
],
"description": "Clean up runs executed before the specified one",
"takes_arg": true,
"arg": {
"name": "run name"
}
},
{
"names": [
"-but"
],
"description": "Clean up all runs except the specified one",
"takes_arg": true,
"arg": {
"name": "run name"
}
},
{
"names": [
"-n",
"-dry-run"
],
"description": "Print names of file to be removed without deleting them (Default: false)"
},
{
"names": [
"-f",
"-force"
],
"description": "Force clean command (Default: false)"
},
{
"names": [
"-h",
"-help"
],
"description": "Print the command usage (Default: false)"
},
{
"names": [
"-k",
"-keep-logs"
],
"description": "Removes only temporary files but retains execution log entries and metadata (Default: false)"
},
{
"names": [
"-q",
"-quiet"
],
"description": "Do not print names of files removed (Default: false)"
}
],
"args": [
{
"name": "run_name|session_id"
}
]
},
{
"name": "clone",
"description": "Clone a project into a folder",
"options": [
{
"names": [
"-h",
"-help"
],
"description": "Print the command usage (Default: false)"
},
{
"names": [
"-hub"
],
"description": "Service hub where the project is hosted (Default: GitHub)",
"takes_arg": true,
"arg": {
"name": "gitlab|github|bitbucket"
}
},
{
"names": [
"-r"
],
"description": "Revision to clone - It can be a git branch, tag or revision number",
"takes_arg": true,
"arg": {
"name": "revision"
}
},
{
"names": [
"-user"
],
"description": "Private repository user name",
"takes_arg": true,
"arg": {
"name": "username"
}
}
],
"args": [
{
"name": "namespace/repository_name"
}
]
},
{
"name": "config",
"description": "Print a project configuration",
"options": [
{
"names": [
"-flat"
],
"description": "Print config using flat notation (Default: false)"
},
{
"names": [
"-h",
"-help"
],
"description": "Print the command usage (Default: false)"
},
{
"names": [
"-profile"
],
"description": "Choose a configuration profile"
},
{
"names": [
"-properties"
],
"description": "Prints config using Java properties notatio (Default: false)"
},
{
"names": [
"-a",
"-show-profiles"
],
"description": "Show all configuration profiles"
},
{
"names": [
"-sort"
],
"description": "Sort config attributes (Default: false)"
}
],
"args": [
{
"name": "project name"
}
]
},
{
"name": "console",
"description": "Launch Nextflow interactive console",
"options": [
{
"names": [
"-h",
"-help"
],
"description": "Print the command usage (Default: false)"
}
]
},
{
"name": "drop",
"description": "Delete the local copy of a project",
"options": [
{
"names": [
"-h",
"-help"
],
"description": "Print the command usage (Default: false)"
},
{
"names": [
"-f"
],
"description": "Delete the repository without taking care of local changes (Default: false)"
}
],
"args": [
{
"name": "name of the project to drop"
}
]
},
{
"name": "help",
"description": "Print the usage help for a command",
"options": [
{
"names": [
"-h",
"-help"
],
"description": "Print the command usage (Default: false)"
}
]
},
{
"name": "info",
"description": "Print project and system runtime information",
"options": [
{
"names": [
"-u",
"-check-updates"
],
"description": "Check for remote updates (Default: false)"
},
{
"names": [
"-d"
],
"description": "Show detailed information (Default: false)"
},
{
"names": [
"-h",
"-help"
],
"description": "Print the command usage (Default: false)"
},
{
"names": [
"-o"
],
"description": "Output format, either: text (default), json, yaml"
}
],
"args": [
{
"name": "project name"
}
]
},
{
"name": "kuberun",
"description": "Execute a workflow in a Kubernetes cluster (experimental)",
"options": [
{
"names": [
"-E"
],
"description": "Exports all current system environment (Default: false)"
},
{
"names": [
"-ansi-log"
],
"description": "Enable/disable ANSI console logging"
},
{
"names": [
"-bucket-dir"
],
"description": "Remote bucket where intermediate result files are stored",
"takes_arg": true,
"arg": {
"name": "remote bucket"
}
},
{
"names": [
"-cache"
],
"description": "Enable/disable processes caching"
},
{
"names": [
"-disable-jobs-cancellation"
],
"description": "Prevent the cancellation of child jobs on execution termination"
},
{
"names": [
"-dsl1"
],
"description": "Execute the workflow using DSL1 syntax (Default: false)"
},
{
"names": [
"-dsl2"
],
"description": "Execute the workflow using DSL2 syntax (Default: false)"
},
{
"names": [
"-dump-channels"
],
"description": "Dump channels for debugging purpose"
},
{
"names": [
"-dump-hashes"
],
"description": "Dump task hash keys for debugging purpose (Default: false)"
},
{
"names": [
"-e"
],
"description": "Add the specified variable to execution environment. Syntax: -e.key=value (Default: {})",
"takes_arg": true,
"arg": {
"name": "key=value"
}
},
{
"names": [
"-entry"
],
"description": "Entry workflow name to be executed",
"takes_arg": true,
"arg": {
"name": "entry workflow name"
}
},
{
"names": [
"-head-cpus"
],
"description": "Specify number of CPUs requested for the Nextflow pod (Default: 0)"
},
{
"names": [
"-head-memory"
],
"description": "Specify amount of memory requested for the Nextflow pod"
},
{
"names": [
"-h",
"-help"
],
"description": "Print the command usage (Default: false)"
},
{
"names": [
"-hub"
],
"description": "Service hub where the project is hosted (Default: github)",
"takes_arg": true,
"arg": {
"name": "service hub"
}
},
{
"names": [
"-latest"
],
"description": "Pull latest changes before run (Default: false)"
},
{
"names": [
"-lib"
],
"description": "Library extension path",
"takes_arg": true,
"arg": {
"name": "library extension path"
}
},
{
"names": [
"-main-script"
],
"description": "The script file to be executed when launching a project directory or repository",
"takes_arg": true,
"arg": {
"name": "script file"
}
},
{
"names": [
"-name"
],
"description": "Assign a mnemonic name to the a pipeline run",
"takes_arg": true,
"arg": {
"name": "name"
}
},
{
"names": [
"-n",
"-namespace"
],
"description": "Specify the K8s namespace to use"
},
{
"names": [
"-offline"
],
"description": "Do not check for remote project updates (Default: false)"
},
{
"names": [
"-params-file"
],
"description": "Load script parameters from a JSON/YAML file",
"takes_arg": true,
"arg": {
"name": "JSON/YAML file",
"template": "filepaths"
}
},
{
"names": [
"-plugins"
],
"description": "Specify the plugins to be applied for this run e.g. nf-amazon,nf-tower",
"takes_arg": true,
"arg": {
"name": "plugins ids separated by comma"
}
},
{
"names": [
"-pod-image"
],
"description": "Specify the container image for the Nextflow pod"
},
{
"names": [
"-process"
],
"description": "Set process options. Syntax: -process.key=value (Default: {}",
"takes_arg": true,
"arg": {
"name": "key=value"
}
},
{
"names": [
"-profile"
],
"description": "Choose a configuration profile",
"takes_arg": true,
"arg": {
"name": "profile"
}
},
{
"names": [
"-qs",
"-queue-size"
],
"description": "Max number of processes that can be executed in parallel by each executor",
"takes_arg": true,
"arg": {
"name": "number"
}
},
{
"names": [
"-remoteProfile"
],
"description": "Choose a configuration profile in the remoteConfig"
},
{
"names": [
"-resume"
],
"description": "Execute the script using the cached results, useful to continue executions that was stopped by an error"
},
{
"names": [
"-r",
"-revision"
],
"description": "Revision of the project to run (either a git branch, tag or commit SHA number)",
"takes_arg": true,
"arg": {
"name": "project revision (tag/branch/hash"
}
},
{
"names": [
"-stub-run",
"-stub"
],
"description": "Execute the workflow replacing process scripts with command stubs (Default: false)"
},
{
"names": [
"-test"
],
"description": "Test a script function with the name specified",
"takes_arg": true,
"arg": {
"name": "name"
}
},
{
"names": [
"-user"
],
"description": "Private repository user name",
"takes_arg": true,
"arg": {
"name": "username"
}
},
{
"names": [
"-v",
"-volume-mount"
],
"description": "Volume claim mounts eg. my-pvc:/mnt/path"
},
{
"names": [
"-with-charliecloud"
],
"description": "Enable process execution in a Charliecloud container runtime"
},
{
"names": [
"-with-conda"
],
"description": "Use the specified Conda environment package or file (must end with .yml|.yaml suffix)",
"takes_arg": true,
"arg": {
"name": "conda .yml/.yaml file"
}
},
{
"names": [
"-with-dag"
],
"description": "Create pipeline DAG file",
"takes_arg": true,
"arg": {
"name": "filename, e.g. dag.dot"
}
},
{
"names": [
"-with-docker"
],
"description": "Enable process execution in a Docker container",
"takes_arg": true,
"arg": {
"name": "a docker container image"
}
},
{
"names": [
"-N",
"-with-notification"
],
"description": "Send a notification email on workflow completion to the specified recipients",
"takes_arg": true,
"arg": {
"name": "email"
}
},
{
"names": [
"-with-podman"
],
"description": "Enable process execution in a Podman container"
},
{
"names": [
"-with-report"
],
"description": "Create processes execution html report",
"takes_arg": true,
"arg": {
"name": "report filename e.g. report.html"
}
},
{
"names": [
"-with-singularity"
],
"description": "Enable process execution in a Singularity container"
},
{
"names": [
"-with-timeline"
],
"description": "Create processes execution timeline file",
"takes_arg": true,
"arg": {
"name": "timeline filename e.g. timeline.html"
}
},
{
"names": [
"-with-tower"
],
"description": "Monitor workflow execution with Seqera Tower service"
},
{
"names": [
"-with-trace"
],
"description": "Create processes execution tracing file",
"takes_arg": true,
"arg": {
"name": "trace text filename e.g. trace.txt"
}
},
{
"names": [
"-with-weblog"
],
"description": "Send workflow status messages via HTTP to target URL",
"takes_arg": true,
"arg": {
"name": "target web URL"
}
},
{
"names": [
"-without-docker"
],
"description": "Disable process execution with Docker (Default: false)"
},
{
"names": [
"-without-podman"
],
"description": "Disable process execution in a Podman container"
},
{
"names": [
"-w",
"-work-dir"
],
"description": "Directory where intermediate result files are stored",
"takes_arg": true,
"arg": {
"name": "work dir"
}
}
],
"args": [
{
"name": "project name"
}
]
},
{
"name": "list",
"description": "List all downloaded projects",
"options": [
{
"names": [
"-h",
"-help"
],
"description": "Print the command usage (Default: false)"
}
]
},
{
"name": "log",
"description": "Print executions log and runtime info",
"options": [
{
"names": [
"-after"
],
"description": "Show log entries for runs executed after the specified one",
"takes_arg": true,
"arg": {
"name": "run name"
}
},
{
"names": [
"-before"
],
"description": "Show log entries for runs executed before the specified one",
"takes_arg": true,
"arg": {
"name": "run name"
}
},
{
"names": [
"-but"
],
"description": "Show log entries of all runs except the specified one",
"takes_arg": true,
"arg": {
"name": "run name"
}
},
{
"names": [
"-f",
"-fields"
],
"description": "Comma separated list of fields to include in the printed log -- Use the `-l` option to show the list of available fields",
"takes_arg": true,
"arg": {
"name": "field1,field2,..."
}
},
{
"names": [
"-F",
"filter"
],
"description": "Filter log entries by a custom expression e.g. process =~ /foo.*/ && status == 'COMPLETED'",
"takes_arg": true,
"arg": {
"name": "expression"
}
},
{
"names": [
"-h",
"-help"
],
"description": "Print the command usage (Default: false)"
},
{
"names": [
"-l",
"-list-fields"
],
"description": "Show all available fields (Default: false)"
},
{
"names": [
"-q",
"-quiet"
],
"description": "Show only run names (Default: false)"
},
{
"names": [
"-s"
],
"description": "Character used to separate column values (Default: )",
"takes_arg": true,
"arg": {
"name": "character"
}
},
{
"names": [
"-t",
"-template"
],
"description": "Text template used to each record in the log",
"takes_arg": true,
"arg": {
"name": "template"
}
}
],
"args": [
{
"name": "run name"
}
]
},
{
"name": "pull",
"description": "Download or update a project",
"options": [
{
"names": [
"-all"
],
"description": "Update all downloaded projects (Default: false)"
},
{
"names": [
"-h",
"-help"
],
"description": "Print the command usage (Default: false)"
},
{
"names": [
"-hub"
],
"description": "Service hub where the project is hosted"
},
{
"names": [
"-r",
"-revision"
],
"description": "Revision of the project to run (either a git branch, tag or commit SHA number)"
},
{
"names": [
"-user"
],
"description": "Private repository user name"
}
],
"args": [
{
"name": "project name or repository url to pull"
}
]
},
{
"name": "run",
"description": "Execute a pipeline project",
"options": [
{
"names": [
"-E"
],
"description": "Exports all current system environment (Default: false)"
},
{
"names": [
"-ansi-log"
],
"description": "Enable/disable ANSI console logging"
},
{
"names": [
"-bucket-dir"
],
"description": "Remote bucket where intermediate result files are stored",
"takes_arg": true,
"arg": {
"name": "remote bucket"
}
},
{
"names": [
"-cache"
],
"description": "Enable/disable processes caching"
},
{
"names": [
"-disable-jobs-cancellation"
],
"description": "Prevent the cancellation of child jobs on execution termination"
},
{
"names": [
"-dsl1"
],
"description": "Execute the workflow using DSL1 syntax (Default: false)"
},
{
"names": [
"-dsl2"
],
"description": "Execute the workflow using DSL2 syntax (Default: false)"
},
{
"names": [
"-dump-channels"
],
"description": "Dump channels for debugging purpose"
},
{
"names": [
"-dump-hashes"
],
"description": "Dump task hash keys for debugging purpose (Default: false)"
},
{
"names": [
"-e."
],
"description": "Add the specified variable to execution environment. Syntax: -e.key=value (Default: {})",
"takes_arg": true,
"arg": {
"name": "key=value"
}
},
{
"names": [
"-entry"
],
"description": "Entry workflow name to be executed",
"takes_arg": true,
"arg": {
"name": "entry workflow name"
}
},
{
"names": [
"-h",
"-help"
],
"description": "Print the command usage (Default: false)"
},
{
"names": [
"-hub"
],
"description": "Service hub where the project is hosted (Default: github)",
"takes_arg": true,
"arg": {
"name": "service hub"
}
},
{
"names": [
"-latest"
],
"description": "Pull latest changes before run (Default: false)"
},
{
"names": [
"-lib"
],
"description": "Library extension path",
"takes_arg": true,
"arg": {
"name": "library extension path"
}
},
{
"names": [
"-main-script"
],
"description": "The script file to be executed when launching a project directory or repository",
"takes_arg": true,
"arg": {
"name": "script file"
}
},
{
"names": [
"-name"
],
"description": "Assign a mnemonic name to the a pipeline run",
"takes_arg": true,
"arg": {
"name": "name"
}
},
{
"names": [
"-offline"
],
"description": "Do not check for remote project updates (Default: false)"
},
{
"names": [
"-params-file"
],
"description": "Load script parameters from a JSON/YAML file",
"takes_arg": true,
"arg": {
"name": "JSON/YAML file",
"template": "filepaths"
}
},
{
"names": [
"-plugins"
],
"description": "Specify the plugins to be applied for this run e.g. nf-amazon,nf-tower",
"takes_arg": true,
"arg": {
"name": "plugins ids separated by comma"
}
},
{
"names": [
"-process."
],
"description": "Set process options. Syntax: -process.key=value (Default: {}",
"takes_arg": true,
"arg": {
"name": "key=value"
}
},
{
"names": [
"-profile"
],
"description": "Choose a configuration profile",
"takes_arg": true,
"arg": {
"name": "profile"
}
},
{
"names": [
"-qs",
"-queue-size"
],
"description": "Max number of processes that can be executed in parallel by each executor",
"takes_arg": true,
"arg": {
"name": "number"
}
},
{
"names": [
"-resume"
],
"description": "Execute the script using the cached results, useful to continue executions that was stopped by an error",
"takes_arg": true,
"arg": {
"name": "session ID"
}
},
{
"names": [
"-r",
"-revision"
],
"description": "Revision of the project to run (either a git branch, tag or commit SHA number)",
"takes_arg": true,
"arg": {
"name": "project revision (tag/branch/hash"
}
},
{
"names": [
"-stub-ru",
"-stub"
],
"description": "Execute the workflow replacing process scripts with command stubs (Default: false)"
},
{
"names": [
"-test"
],
"description": "Test a script function with the name specified",
"takes_arg": true,
"arg": {
"name": "name"
}
},
{
"names": [
"-user"
],
"description": "Private repository user name",
"takes_arg": true,
"arg": {
"name": "username"
}
},
{
"names": [
"-with-charliecloud"
],
"description": "Enable process execution in a Charliecloud container runtime"
},
{
"names": [
"-with-conda"
],
"description": "Use the specified Conda environment package or file (must end with .yml|.yaml suffix)",
"takes_arg": true,
"arg": {
"name": "conda .yml/.yaml file"
}
},
{
"names": [
"-with-dag"
],
"description": "Create pipeline DAG file",
"takes_arg": true,
"arg": {
"name": "filename, e.g. dag.dot"
}
},
{
"names": [
"-with-docker"
],
"description": "Enable process execution in a Docker container",
"takes_arg": true,
"arg": {
"name": "a docker container image"
}
},
{
"names": [
"-N",
"-with-notification"
],
"description": "Send a notification email on workflow completion to the specified recipients",
"takes_arg": true,
"arg": {
"name": "email"
}
},
{
"names": [
"-with-podman"
],
"description": "Enable process execution in a Podman container"
},
{
"names": [
"-with-report"
],
"description": "Create processes execution html report",
"takes_arg": true,
"arg": {
"name": "report filename e.g. report.html"
}
},
{
"names": [
"-with-singularity"
],
"description": "Enable process execution in a Singularity container"
},
{
"names": [
"-with-timeline"
],
"description": "Create processes execution timeline file",
"takes_arg": true,
"arg": {
"name": "timeline filename e.g. timeline.html"
}
},
{
"names": [
"-with-tower"
],
"description": "Monitor workflow execution with Seqera Tower service"
},
{
"names": [
"-with-trace"
],
"description": "Create processes execution tracing file",
"takes_arg": true,
"arg": {
"name": "trace text filename e.g. trace.txt"
}
},
{
"names": [
"-with-weblog"
],
"description": "Send workflow status messages via HTTP to target URL",
"takes_arg": true,
"arg": {
"name": "target web URL"
}
},
{
"names": [
"-without-docker"
],
"description": "Disable process execution with Docker (Default: false)"
},
{
"names": [
"-without-podman"
],
"description": "Disable process execution in a Podman container"
},
{
"names": [
"-w",
"-work-dir"
],
"description": "Directory where intermediate result files are stored",
"takes_arg": true,
"arg": {
"name": "work dir"
}
}
],
"args": [
{
"name": "project name, repository url, or local path"
}
]
},
{
"name": "secrets",
"description": "Handle and manage sensitive information for pipeline execution in a safe manner",
"options": [
{
"names": [
"list"
],
"description": "List secrets available in the current store e.g. nextflow secrets list"
},
{
"names": [
"get"
],
"description": "Allows retrieving a secret value e.g. nextflow secrets get FOO",
"takes_arg": true,
"arg": {
"name": "secret name"
}
},
{
"names": [
"set"
],
"description": "Allows creating creating a new secret or overriding an existing one e.g. nextflow secrets set FOO \"Hello world\"",
"takes_arg": true,
"arg": {
"name": "secret name and value"
}
},
{
"names": [
"delete"
],
"description": "Allows deleting an existing secret e.g. nextflow secrets delete FOO",
"takes_arg": true,
"arg": {
"name": "secret name"
}
}
]
},
{
"name": "self-update",
"description": "Update nextflow runtime to the latest available version",
"options": [
{
"names": [
"-h",
"-help"
],
"description": "Print the command usage (Default: false)"
}
]
},
{
"name": "view",
"description": "View project script file(s)",
"options": [
{
"names": [
"-h",
"-help"
],
"description": "Print the command usage (Default: false)"
},
{
"names": [
"-l"
],
"description": "List repository content (Default: false)"
},
{
"names": [
"-q"
],
"description": "Hide header line (Default: false)"
}
],
"args": [
{
"name": "project name"
}
]
}
],
"options": [
{
"names": [
"-C"
],
"description": "Use the specified configuration file(s) overriding any defaults",
"takes_arg": true,
"arg": {
"name": "configuration file",
"template": "filepaths"
}
},
{
"names": [
"-D"
],
"description": "Set JVM properties",
"takes_arg": true,
"arg": {
"name": "custom Java system property"
}
},
{
"names": [
"-bg"
],
"description": "Execute nextflow in background"
},
{
"names": [
"-c",
"-config"
],
"description": "Add the specified file to configuration set",
"takes_arg": true,
"arg": {
"name": "configuration file",
"template": "filepaths"
}
},
{
"names": [
"-d",
"-dockerize"
],
"description": "Launch nextflow via Docker (experimental)"
},
{
"names": [
"-h"
],
"description": "Print this help"
},
{
"names": [
"-log"
],
"description": "Set nextflow log file path"
},
{
"names": [
"-q",
"-quiet"
],
"description": "Do not print information messages"
},
{
"names": [
"-syslog"
],
"description": "Send logs to syslog server (eg. localhost:514)"
},
{
"names": [
"-v",
"-version"
],
"description": "Print the program version"
}
]
}